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<h3>
Andreas Tille pushed to branch upstream
at <a href="https://salsa.debian.org/med-team/python-misopy">Debian Med / python-misopy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/python-misopy/commit/a7cdbd7f99b285512161da0606ad2ca6fdc23820">a7cdbd7f</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-10-30T06:29:06Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 0.5.4+dfsg</pre>
</li>
</ul>
<h4>16 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#8875df48c18030126ef5ef5a6f5c93b23451fb9f">
<span class="new-file">
+
MANIFEST.in
</span>
</a>
</li>
<li class="file-stats">
<a href="#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
PKG-INFO
</a>
</li>
<li class="file-stats">
<a href="#43c7c92008c8bfc0619e6072605e938a414ac992">
<span class="new-file">
+
misopy.egg-info/PKG-INFO
</span>
</a>
</li>
<li class="file-stats">
<a href="#4e778be103cb209ef5d4a24f32f38874c9a9e0f4">
<span class="new-file">
+
misopy.egg-info/SOURCES.txt
</span>
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</li>
<li class="file-stats">
<a href="#fb040da79a7aff1e3e67e811ec899afe5c266d98">
<span class="new-file">
+
misopy.egg-info/dependency_links.txt
</span>
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</li>
<li class="file-stats">
<a href="#1a40118b5ed60ad385d5eb0481c7ddebd0679f71">
<span class="new-file">
+
misopy.egg-info/entry_points.txt
</span>
</a>
</li>
<li class="file-stats">
<a href="#d3501251e5d8a05c0a6da10196989115a4fbfff5">
<span class="new-file">
+
misopy.egg-info/pbr.json
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<li class="file-stats">
<a href="#be920f71f2454be34a65851469fe00eba836f7ce">
<span class="new-file">
+
misopy.egg-info/requires.txt
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<li class="file-stats">
<a href="#4d078d84dfc1124c1411b710372c8da49cce0691">
<span class="new-file">
+
misopy.egg-info/top_level.txt
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</li>
<li class="file-stats">
<a href="#31e5beed9ddf5f689e1706d33342d7a227f4f30a">
misopy/__init__.py
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</li>
<li class="file-stats">
<a href="#51743c8a5dd4ae7a5e3ff4be7f2dcea923a7cee0">
misopy/credible_intervals.py
</a>
</li>
<li class="file-stats">
<a href="#81ef9be5184376161a1e82feac36f3768007cdbe">
misopy/run_events_analysis.py
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</li>
<li class="file-stats">
<a href="#db070d7c8c5a7d9163c5110129e29cd6f14df2ed">
misopy/samples_utils.py
</a>
</li>
<li class="file-stats">
<a href="#84d5450da339c483f205f0e34adc7fca5353997c">
pysplicing/src/miso.c
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<li class="file-stats">
<a href="#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f">
<span class="new-file">
+
setup.cfg
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</li>
<li class="file-stats">
<a href="#8e2edce0d507e1297474f25c00cae94258db38d8">
setup.py
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="8875df48c18030126ef5ef5a6f5c93b23451fb9f">
<a href="https://salsa.debian.org/med-team/python-misopy/commit/a7cdbd7f99b285512161da0606ad2ca6fdc23820#8875df48c18030126ef5ef5a6f5c93b23451fb9f"><strong>MANIFEST.in</strong></a>
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">include pysplicing/include/*</span>
</pre>
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">include pysplicing/src/f2c/*</span>
</pre>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">include pysplicing/src/lapack/*</span>
</pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">include misopy/settings/*</span>
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">include misopy/sashimi_plot/settings/*</span>
</pre>
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">include misopy/sashimi_plot/test-data/*</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">include misopy/sashimi_plot/test-data/bam-data/*</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">include misopy/sashimi_plot/test-data/miso-data/*</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">include misopy/sashimi_plot/test-data/miso-data/heartKOa/chr17/*</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">include misopy/sashimi_plot/test-data/miso-data/heartKOb/chr17/*</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">include misopy/sashimi_plot/test-data/miso-data/heartWT1/chr17/*</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">include misopy/sashimi_plot/test-data/miso-data/heartWT2/chr17/*</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">include misopy/gff-events/mm9/*</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">include misopy/gff-events/mm9/genes/*</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">include misopy/test-data/sam-data/*</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">include misopy/test-data/se-counts/*</span></pre>
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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">\ No newline at end of file</td>
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<li id="7d26833a43d8865f6d9679068f6f9ee7d6e13dcf">
<a href="https://salsa.debian.org/med-team/python-misopy/commit/a7cdbd7f99b285512161da0606ad2ca6fdc23820#7d26833a43d8865f6d9679068f6f9ee7d6e13dcf"><strong>PKG-INFO</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">Name: misopy</span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext">Version: 0.5.<span class="idiff left right">3</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 0.5.<span class="idiff left right">4</span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">Summary: Mixture of Isoforms model (MISO) for isoform quantitation using RNA-Seq</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">Home-page: http://genes.mit.edu/burgelab/miso/</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">Author: Yarden Katz</span>
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<a href="https://salsa.debian.org/med-team/python-misopy/commit/a7cdbd7f99b285512161da0606ad2ca6fdc23820#43c7c92008c8bfc0619e6072605e938a414ac992"><strong>misopy.egg-info/PKG-INFO</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Metadata-Version: 1.1</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Name: misopy</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Version: 0.5.4</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Summary: Mixture of Isoforms model (MISO) for isoform quantitation using RNA-Seq</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">Home-page: http://genes.mit.edu/burgelab/miso/</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">Author: Yarden Katz</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">Author-email: yarden@mit.edu</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">License: UNKNOWN</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Description: MISO (Mixture of Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples. By modeling the generative process by which reads are produced from isoforms in RNA-Seq, the MISO model uses Bayesian inference to compute the probability that a read originated from a particular isoform.</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> MISO uses the inferred assignment of reads to isoforms to quantitate the abundances of the underlying set of alternative mRNA isoforms. Confidence intervals over estimates can be obtained, which quantify the reliability of the estimates. </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> Please see http://genes.mit.edu/burgelab/miso/docs/ for MISO manual and documentation.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">Keywords: bioinformatics,sequence analysis,alternative splicing,RNA-Seq,probabilistic models,bayesian</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">Platform: ALL</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Classifier: Development Status :: 4 - Beta</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Classifier: Intended Audience :: Science/Research</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">Classifier: Programming Language :: C</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">Classifier: Programming Language :: Python</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">Classifier: Topic :: Scientific/Engineering :: Bio-Informatics</span></pre>
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<a href="https://salsa.debian.org/med-team/python-misopy/commit/a7cdbd7f99b285512161da0606ad2ca6fdc23820#4e778be103cb209ef5d4a24f32f38874c9a9e0f4"><strong>misopy.egg-info/SOURCES.txt</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">MANIFEST.in</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">README</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">setup.py</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">misopy/Gene.py</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">misopy/__init__.py</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">misopy/as_events.py</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">misopy/cluster_utils.py</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">misopy/compare_miso.py</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">misopy/credible_intervals.py</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">misopy/exon_utils.py</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">misopy/filter_events.py</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">misopy/gff_utils.py</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">misopy/hypothesis_test.py</span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">misopy/index_gff.py</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">misopy/json_utils.py</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">misopy/kde_subclass.py</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">misopy/legacy_test_pysplicing.py</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">misopy/misc_utils.py</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext">misopy/miso.py</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">misopy/miso_db.py</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext">misopy/miso_pack.py</span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">misopy/miso_sampler.py</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">misopy/miso_utils.py</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">misopy/miso_zip.py</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">misopy/module_availability.py</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">misopy/parse_csv.py</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">misopy/parse_gene.py</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">misopy/pe_utils.py</span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">misopy/pickle_utils.py</span>
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30
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">misopy/py2c_gene.py</span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">misopy/read_simulator.py</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">misopy/reads_utils.py</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">misopy/run_events_analysis.py</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">misopy/run_miso.py</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext">misopy/sam_rpkm.py</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">misopy/sam_to_bam.py</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext">misopy/sam_utils.py</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">misopy/samples_utils.py</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">misopy/settings.py</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">misopy/summarize_miso.py</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext">misopy/test_cluster.py</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">misopy/test_miso.py</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">misopy.egg-info/PKG-INFO</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">misopy.egg-info/SOURCES.txt</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext">misopy.egg-info/dependency_links.txt</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">misopy.egg-info/entry_points.txt</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">misopy.egg-info/pbr.json</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">misopy.egg-info/requires.txt</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">misopy.egg-info/top_level.txt</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext">misopy/gff-events/mm9/SE.mm9.gff</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">misopy/gff-events/mm9/genes/Atp2b1.mm9.gff</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">misopy/sashimi_plot/Sashimi.py</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">misopy/sashimi_plot/__init__.py</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext">misopy/sashimi_plot/plot.py</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">misopy/sashimi_plot/sashimi_plot.py</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">misopy/sashimi_plot/plot_utils/__init__.py</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">misopy/sashimi_plot/plot_utils/plot_gene.py</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">misopy/sashimi_plot/plot_utils/plot_settings.py</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext">misopy/sashimi_plot/plot_utils/plotting.py</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">misopy/sashimi_plot/plot_utils/samples_plotter.py</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">misopy/sashimi_plot/settings/sashimi_plot_settings.txt</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">misopy/sashimi_plot/test-data/events.gff</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">misopy/sashimi_plot/test-data/bam-data/heartKOa.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">misopy/sashimi_plot/test-data/bam-data/heartKOa.sorted.bam</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">misopy/sashimi_plot/test-data/bam-data/heartKOa.sorted.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext">misopy/sashimi_plot/test-data/bam-data/heartKOb.sorted.bam</span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext">misopy/sashimi_plot/test-data/bam-data/heartKOb.sorted.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">misopy/sashimi_plot/test-data/bam-data/heartWT1.sorted.bam</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext">misopy/sashimi_plot/test-data/bam-data/heartWT1.sorted.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext">misopy/sashimi_plot/test-data/bam-data/heartWT2.sorted.bam</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext">misopy/sashimi_plot/test-data/bam-data/heartWT2.sorted.bam.bai</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">misopy/sashimi_plot/test-data/miso-data/heartKOa/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext">misopy/sashimi_plot/test-data/miso-data/heartKOb/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext">misopy/sashimi_plot/test-data/miso-data/heartWT1/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext">misopy/sashimi_plot/test-data/miso-data/heartWT2/chr17/chr17:45816186:45816265:-@chr17:45815912:45815950:-@chr17:45814875:45814965:-.miso</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">misopy/settings/miso_settings.txt</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext">misopy/test-data/sam-data/c2c12.Atp2b1.sam</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext">pysplicing/include/f2c.h</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext">pysplicing/include/matrix.pmt</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext">pysplicing/include/pyerror.h</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext">pysplicing/include/pysplicing.h</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext">pysplicing/include/random.h</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext">pysplicing/include/splicing.h</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext">pysplicing/include/splicing_error.h</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext">pysplicing/include/splicing_lapack.h</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext">pysplicing/include/splicing_matrix.h</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext">pysplicing/include/splicing_matrix_pmt.h</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext">pysplicing/include/splicing_memory.h</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext">pysplicing/include/splicing_pmt.h</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext">pysplicing/include/splicing_pmt_off.h</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext">pysplicing/include/splicing_random.h</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext">pysplicing/include/splicing_vector.h</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext">pysplicing/include/splicing_vector_pmt.h</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext">pysplicing/include/vector.pmt</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext">pysplicing/pysplicing/__init__.py</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext">pysplicing/src/assignment.c</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext">pysplicing/src/blas.c</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext">pysplicing/src/complexity.c</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext">pysplicing/src/convert.c</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext">pysplicing/src/error.c</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext">pysplicing/src/fortran_stuff.c</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext">pysplicing/src/gff.c</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext">pysplicing/src/ident.c</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext">pysplicing/src/lapack.c</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext">pysplicing/src/lawson_hanson_nnls.c</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext">pysplicing/src/matrix.c</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext">pysplicing/src/memory.c</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext">pysplicing/src/miso.c</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext">pysplicing/src/miso_paired.c</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext">pysplicing/src/nnls.c</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">pysplicing/src/pyconvert.c</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">pysplicing/src/pyerror.c</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext">pysplicing/src/pyrandom.c</span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">pysplicing/src/pysplicing.c</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext">pysplicing/src/qsort.c</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext">pysplicing/src/qsort_r.c</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext">pysplicing/src/random.c</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext">pysplicing/src/simulator.c</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext">pysplicing/src/solve.c</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext">pysplicing/src/strvector.c</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext">pysplicing/src/util.c</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext">pysplicing/src/vector.c</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext">pysplicing/src/f2c/Notice</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext">pysplicing/src/f2c/README</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext">pysplicing/src/f2c/abort_.c</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext">pysplicing/src/f2c/arith.h</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">pysplicing/src/f2c/backspac.c</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">pysplicing/src/f2c/c_abs.c</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="plaintext">pysplicing/src/f2c/c_cos.c</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="plaintext">pysplicing/src/f2c/c_div.c</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">pysplicing/src/f2c/c_exp.c</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext">pysplicing/src/f2c/c_log.c</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">pysplicing/src/f2c/c_sin.c</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext">pysplicing/src/f2c/c_sqrt.c</span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">pysplicing/src/f2c/cabs.c</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext">pysplicing/src/f2c/changes</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext">pysplicing/src/f2c/close.c</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext">pysplicing/src/f2c/comptry.bat</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">pysplicing/src/f2c/ctype.c</span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext">pysplicing/src/f2c/d_abs.c</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext">pysplicing/src/f2c/d_acos.c</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext">pysplicing/src/f2c/d_asin.c</span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext">pysplicing/src/f2c/d_atan.c</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext">pysplicing/src/f2c/d_atn2.c</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">pysplicing/src/f2c/d_cnjg.c</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext">pysplicing/src/f2c/d_cos.c</span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext">pysplicing/src/f2c/d_cosh.c</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext">pysplicing/src/f2c/d_dim.c</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">pysplicing/src/f2c/d_exp.c</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext">pysplicing/src/f2c/d_imag.c</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext">pysplicing/src/f2c/d_int.c</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext">pysplicing/src/f2c/d_lg10.c</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext">pysplicing/src/f2c/d_log.c</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext">pysplicing/src/f2c/d_mod.c</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext">pysplicing/src/f2c/d_nint.c</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext">pysplicing/src/f2c/d_prod.c</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext">pysplicing/src/f2c/d_sin.c</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext">pysplicing/src/f2c/d_sinh.c</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext">pysplicing/src/f2c/d_sqrt.c</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext">pysplicing/src/f2c/d_tan.c</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext">pysplicing/src/f2c/d_tanh.c</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="plaintext">pysplicing/src/f2c/derf_.c</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext">pysplicing/src/f2c/derfc_.c</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext">pysplicing/src/f2c/dfe.c</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext">pysplicing/src/f2c/dolio.c</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext">pysplicing/src/f2c/dtime_.c</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext">pysplicing/src/f2c/due.c</span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext">pysplicing/src/f2c/dummy.c</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext">pysplicing/src/f2c/ef1asc_.c</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext">pysplicing/src/f2c/ef1cmc_.c</span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext">pysplicing/src/f2c/endfile.c</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext">pysplicing/src/f2c/erf_.c</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext">pysplicing/src/f2c/erfc_.c</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext">pysplicing/src/f2c/err.c</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">pysplicing/src/f2c/etime_.c</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext">pysplicing/src/f2c/exit_.c</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext">pysplicing/src/f2c/f2c.h</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext">pysplicing/src/f2c/f2c.h0</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext">pysplicing/src/f2c/f2ch.add</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext">pysplicing/src/f2c/f77_aloc.c</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext">pysplicing/src/f2c/f77vers.c</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext">pysplicing/src/f2c/fctype.h</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="plaintext">pysplicing/src/f2c/fio.h</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext">pysplicing/src/f2c/fmt.c</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext">pysplicing/src/f2c/fmt.h</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext">pysplicing/src/f2c/fmtlib.c</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext">pysplicing/src/f2c/fp.h</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext">pysplicing/src/f2c/ftell_.c</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext">pysplicing/src/f2c/getarg_.c</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext">pysplicing/src/f2c/getenv_.c</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext">pysplicing/src/f2c/h_abs.c</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext">pysplicing/src/f2c/h_dim.c</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext">pysplicing/src/f2c/h_dnnt.c</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="plaintext">pysplicing/src/f2c/h_indx.c</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="plaintext">pysplicing/src/f2c/h_len.c</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="plaintext">pysplicing/src/f2c/h_mod.c</span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="plaintext">pysplicing/src/f2c/h_nint.c</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="plaintext">pysplicing/src/f2c/h_sign.c</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="plaintext">pysplicing/src/f2c/hl_ge.c</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="plaintext">pysplicing/src/f2c/hl_gt.c</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="plaintext">pysplicing/src/f2c/hl_le.c</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="plaintext">pysplicing/src/f2c/hl_lt.c</span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="plaintext">pysplicing/src/f2c/i77vers.c</span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="plaintext">pysplicing/src/f2c/i_abs.c</span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="plaintext">pysplicing/src/f2c/i_dim.c</span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="plaintext">pysplicing/src/f2c/i_dnnt.c</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="plaintext">pysplicing/src/f2c/i_indx.c</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="plaintext">pysplicing/src/f2c/i_len.c</span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="plaintext">pysplicing/src/f2c/i_mod.c</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="plaintext">pysplicing/src/f2c/i_nint.c</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="plaintext">pysplicing/src/f2c/i_sign.c</span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="plaintext">pysplicing/src/f2c/iargc_.c</span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="plaintext">pysplicing/src/f2c/iio.c</span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="plaintext">pysplicing/src/f2c/ilnw.c</span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="plaintext">pysplicing/src/f2c/inquire.c</span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="plaintext">pysplicing/src/f2c/l_ge.c</span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="plaintext">pysplicing/src/f2c/l_gt.c</span>
</pre>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="plaintext">pysplicing/src/f2c/l_le.c</span>
</pre>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="plaintext">pysplicing/src/f2c/l_lt.c</span>
</pre>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="plaintext">pysplicing/src/f2c/lbitbits.c</span>
</pre>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="plaintext">pysplicing/src/f2c/lbitshft.c</span>
</pre>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="plaintext">pysplicing/src/f2c/libf2c.lbc</span>
</pre>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="plaintext">pysplicing/src/f2c/libf2c.sy</span>
</pre>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="plaintext">pysplicing/src/f2c/lio.h</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="plaintext">pysplicing/src/f2c/lread.c</span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="plaintext">pysplicing/src/f2c/lwrite.c</span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="plaintext">pysplicing/src/f2c/main.c</span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="plaintext">pysplicing/src/f2c/makefile.sy</span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="plaintext">pysplicing/src/f2c/makefile.u</span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="plaintext">pysplicing/src/f2c/makefile.vc</span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="plaintext">pysplicing/src/f2c/makefile.wat</span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="plaintext">pysplicing/src/f2c/math.hvc</span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="plaintext">pysplicing/src/f2c/mkfile.plan9</span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="plaintext">pysplicing/src/f2c/open.c</span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="plaintext">pysplicing/src/f2c/pow_ci.c</span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="plaintext">pysplicing/src/f2c/pow_dd.c</span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="plaintext">pysplicing/src/f2c/pow_di.c</span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="plaintext">pysplicing/src/f2c/pow_hh.c</span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="plaintext">pysplicing/src/f2c/pow_ii.c</span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="plaintext">pysplicing/src/f2c/pow_ri.c</span>
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241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="plaintext">pysplicing/src/f2c/pow_zi.c</span>
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242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="plaintext">pysplicing/src/f2c/pow_zz.c</span>
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243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="plaintext">pysplicing/src/f2c/r_abs.c</span>
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244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="plaintext">pysplicing/src/f2c/r_acos.c</span>
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245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="plaintext">pysplicing/src/f2c/r_asin.c</span>
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246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="plaintext">pysplicing/src/f2c/r_atan.c</span>
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247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="plaintext">pysplicing/src/f2c/r_atn2.c</span>
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248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="plaintext">pysplicing/src/f2c/r_cnjg.c</span>
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249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="plaintext">pysplicing/src/f2c/r_cos.c</span>
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250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="plaintext">pysplicing/src/f2c/r_cosh.c</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="plaintext">pysplicing/src/f2c/r_dim.c</span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="plaintext">pysplicing/src/f2c/r_exp.c</span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="plaintext">pysplicing/src/f2c/r_imag.c</span>
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254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="plaintext">pysplicing/src/f2c/r_int.c</span>
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255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="plaintext">pysplicing/src/f2c/r_lg10.c</span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="plaintext">pysplicing/src/f2c/r_log.c</span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="plaintext">pysplicing/src/f2c/r_mod.c</span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="plaintext">pysplicing/src/f2c/r_nint.c</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="plaintext">pysplicing/src/f2c/r_sign.c</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="plaintext">pysplicing/src/f2c/r_sin.c</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="plaintext">pysplicing/src/f2c/r_sinh.c</span>
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262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="plaintext">pysplicing/src/f2c/r_sqrt.c</span>
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263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="plaintext">pysplicing/src/f2c/r_tan.c</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="plaintext">pysplicing/src/f2c/r_tanh.c</span>
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265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="plaintext">pysplicing/src/f2c/rawio.h</span>
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266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="plaintext">pysplicing/src/f2c/rdfmt.c</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="plaintext">pysplicing/src/f2c/rewind.c</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="plaintext">pysplicing/src/f2c/rsfe.c</span>
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269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="plaintext">pysplicing/src/f2c/rsli.c</span>
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270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="plaintext">pysplicing/src/f2c/rsne.c</span>
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271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="plaintext">pysplicing/src/f2c/s_cat.c</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="plaintext">pysplicing/src/f2c/s_cmp.c</span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="plaintext">pysplicing/src/f2c/s_copy.c</span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="plaintext">pysplicing/src/f2c/s_paus.c</span>
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275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="plaintext">pysplicing/src/f2c/s_rnge.c</span>
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276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="plaintext">pysplicing/src/f2c/s_stop.c</span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="plaintext">pysplicing/src/f2c/scomptry.bat</span>
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278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="plaintext">pysplicing/src/f2c/sfe.c</span>
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279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="plaintext">pysplicing/src/f2c/sig_die.c</span>
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280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="plaintext">pysplicing/src/f2c/signal1.h</span>
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281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="plaintext">pysplicing/src/f2c/signal1.h0</span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="plaintext">pysplicing/src/f2c/signal_.c</span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="plaintext">pysplicing/src/f2c/signbit.c</span>
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284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="plaintext">pysplicing/src/f2c/sue.c</span>
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285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="plaintext">pysplicing/src/f2c/sysdep1.h</span>
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286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="plaintext">pysplicing/src/f2c/sysdep1.h0</span>
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287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="plaintext">pysplicing/src/f2c/system_.c</span>
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288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="plaintext">pysplicing/src/f2c/typesize.c</span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="plaintext">pysplicing/src/f2c/uio.c</span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="plaintext">pysplicing/src/f2c/uninit.c</span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="plaintext">pysplicing/src/f2c/util.c</span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="plaintext">pysplicing/src/f2c/wref.c</span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="plaintext">pysplicing/src/f2c/wrtfmt.c</span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="plaintext">pysplicing/src/f2c/wsfe.c</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="plaintext">pysplicing/src/f2c/wsle.c</span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="plaintext">pysplicing/src/f2c/wsne.c</span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="plaintext">pysplicing/src/f2c/xsum0.out</span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="plaintext">pysplicing/src/f2c/xwsne.c</span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="plaintext">pysplicing/src/f2c/z_abs.c</span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="plaintext">pysplicing/src/f2c/z_cos.c</span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="plaintext">pysplicing/src/f2c/z_div.c</span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="plaintext">pysplicing/src/f2c/z_exp.c</span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="plaintext">pysplicing/src/f2c/z_log.c</span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="plaintext">pysplicing/src/f2c/z_sin.c</span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="plaintext">pysplicing/src/f2c/z_sqrt.c</span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="plaintext">pysplicing/src/lapack/blas.inc</span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="plaintext">pysplicing/src/lapack/dbdsdc.c</span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="plaintext">pysplicing/src/lapack/dbdsqr.c</span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="plaintext">pysplicing/src/lapack/dcopy.c</span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="plaintext">pysplicing/src/lapack/ddot.c</span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="plaintext">pysplicing/src/lapack/debug.h</span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="plaintext">pysplicing/src/lapack/dgebd2.c</span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="plaintext">pysplicing/src/lapack/dgebrd.c</span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="plaintext">pysplicing/src/lapack/dgelq2.c</span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="plaintext">pysplicing/src/lapack/dgelqf.c</span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="plaintext">pysplicing/src/lapack/dgemm.c</span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="plaintext">pysplicing/src/lapack/dgemv.c</span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="plaintext">pysplicing/src/lapack/dgeqr2.c</span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="plaintext">pysplicing/src/lapack/dgeqrf.c</span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="plaintext">pysplicing/src/lapack/dger.c</span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="plaintext">pysplicing/src/lapack/dgesdd.c</span>
</pre>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="plaintext">pysplicing/src/lapack/disnan.c</span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="plaintext">pysplicing/src/lapack/dlabrd.c</span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="plaintext">pysplicing/src/lapack/dlacpy.c</span>
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325
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="plaintext">pysplicing/src/lapack/dlaed6.c</span>
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326
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="plaintext">pysplicing/src/lapack/dlaisnan.c</span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="plaintext">pysplicing/src/lapack/dlamch.c</span>
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328
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="plaintext">pysplicing/src/lapack/dlamrg.c</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="plaintext">pysplicing/src/lapack/dlange.c</span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="plaintext">pysplicing/src/lapack/dlanst.c</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="plaintext">pysplicing/src/lapack/dlapy2.c</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="plaintext">pysplicing/src/lapack/dlarf.c</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="plaintext">pysplicing/src/lapack/dlarfb.c</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="plaintext">pysplicing/src/lapack/dlarfg.c</span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="plaintext">pysplicing/src/lapack/dlarft.c</span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="plaintext">pysplicing/src/lapack/dlartg.c</span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="plaintext">pysplicing/src/lapack/dlas2.c</span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="plaintext">pysplicing/src/lapack/dlascl.c</span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="plaintext">pysplicing/src/lapack/dlasd0.c</span>
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340
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="plaintext">pysplicing/src/lapack/dlasd1.c</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="plaintext">pysplicing/src/lapack/dlasd2.c</span>
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342
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="plaintext">pysplicing/src/lapack/dlasd3.c</span>
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343
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="plaintext">pysplicing/src/lapack/dlasd4.c</span>
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344
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="plaintext">pysplicing/src/lapack/dlasd5.c</span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="plaintext">pysplicing/src/lapack/dlasd6.c</span>
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346
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="plaintext">pysplicing/src/lapack/dlasd7.c</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="plaintext">pysplicing/src/lapack/dlasd8.c</span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="plaintext">pysplicing/src/lapack/dlasda.c</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="plaintext">pysplicing/src/lapack/dlasdq.c</span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="plaintext">pysplicing/src/lapack/dlasdt.c</span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="plaintext">pysplicing/src/lapack/dlaset.c</span>
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352
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="plaintext">pysplicing/src/lapack/dlasq1.c</span>
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353
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="plaintext">pysplicing/src/lapack/dlasq2.c</span>
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354
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="plaintext">pysplicing/src/lapack/dlasq3.c</span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="plaintext">pysplicing/src/lapack/dlasq4.c</span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="plaintext">pysplicing/src/lapack/dlasq5.c</span>
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357
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="plaintext">pysplicing/src/lapack/dlasq6.c</span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="plaintext">pysplicing/src/lapack/dlasr.c</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="plaintext">pysplicing/src/lapack/dlasrt.c</span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="plaintext">pysplicing/src/lapack/dlassq.c</span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="plaintext">pysplicing/src/lapack/dlasv2.c</span>
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362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="plaintext">pysplicing/src/lapack/dnrm2.c</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="plaintext">pysplicing/src/lapack/dorg2r.c</span>
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364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="plaintext">pysplicing/src/lapack/dorgbr.c</span>
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365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="plaintext">pysplicing/src/lapack/dorgl2.c</span>
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366
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="plaintext">pysplicing/src/lapack/dorglq.c</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="plaintext">pysplicing/src/lapack/dorgqr.c</span>
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368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="plaintext">pysplicing/src/lapack/dorm2r.c</span>
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369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="plaintext">pysplicing/src/lapack/dormbr.c</span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="plaintext">pysplicing/src/lapack/dorml2.c</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="plaintext">pysplicing/src/lapack/dormlq.c</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="plaintext">pysplicing/src/lapack/dormqr.c</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="plaintext">pysplicing/src/lapack/drot.c</span>
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374
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="plaintext">pysplicing/src/lapack/dscal.c</span>
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375
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="plaintext">pysplicing/src/lapack/dswap.c</span>
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376
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="plaintext">pysplicing/src/lapack/dtrmm.c</span>
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377
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="plaintext">pysplicing/src/lapack/dtrmv.c</span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="plaintext">pysplicing/src/lapack/ieeeck.c</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="plaintext">pysplicing/src/lapack/iladlc.c</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="plaintext">pysplicing/src/lapack/iladlr.c</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="plaintext">pysplicing/src/lapack/ilaenv.c</span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="plaintext">pysplicing/src/lapack/iparmq.c</span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="plaintext">pysplicing/src/lapack/lapack.inc</span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="plaintext">pysplicing/src/lapack/len_trim.c</span>
</pre>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="plaintext">pysplicing/src/lapack/lsame.c</span>
</pre>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="plaintext">pysplicing/src/lapack/stat.h</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="plaintext">pysplicing/src/lapack/xerbla.c</span></pre>
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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">\ No newline at end of file</td>
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<a href="https://salsa.debian.org/med-team/python-misopy/commit/a7cdbd7f99b285512161da0606ad2ca6fdc23820#fb040da79a7aff1e3e67e811ec899afe5c266d98"><strong>misopy.egg-info/dependency_links.txt</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-misopy/commit/a7cdbd7f99b285512161da0606ad2ca6fdc23820#1a40118b5ed60ad385d5eb0481c7ddebd0679f71"><strong>misopy.egg-info/entry_points.txt</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[console_scripts]</span>
</pre>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">compare_miso = misopy.compare_miso:main</span>
</pre>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">exon_utils = misopy.exon_utils:main</span>
</pre>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">filter_events = misopy.filter_events:main</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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5
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">index_gff = misopy.index_gff:main</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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6
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">miso = misopy.miso:main</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">miso_pack = misopy.miso_pack:main</span>
</pre>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">miso_zip = misopy.miso_zip:main</span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" 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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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">module_availability = misopy.module_availability:main</span>
</pre>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">pe_utils = misopy.pe_utils:main</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">plot.py = misopy.sashimi_plot.plot:main</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">run_events_analysis.py = misopy.run_events_analysis:main</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">run_miso.py = misopy.run_miso:main</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">sam_to_bam = misopy.sam_to_bam:main</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">sashimi_plot = misopy.sashimi_plot.sashimi_plot:main</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">summarize_miso = misopy.summarize_miso:main</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">test_miso = misopy.test_miso:main</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="json"><span class="p">{</span><span class="s2" style="color: #d14;">"is_release"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="kc" style="font-weight: 600;">false</span><span class="p">,</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"git_version"</span><span class="p">:</span><span class="w" style="color: #bbb;"> </span><span class="s2" style="color: #d14;">"b644df6"</span><span class="p">}</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">matplotlib</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">numpy >= 1.5.0</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">scipy >= 0.9.0</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">pysam >= 0.6.0</span></pre>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">misopy</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">pysplicing</span></pre>
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<pre style="margin: 0;">-<span id="LC1" 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;">"0.5.<span class="idiff left right">3</span>"</span></span></pre>
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<pre style="margin: 0;">+<span id="LC1" 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;">"0.5.<span class="idiff left right">4</span>"</span></span></pre>
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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">@@ -43,10 +43,10 @@ def compute_credible_intervals(samples, confidence_level=.95):</td>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># compute the lower bound of the interval</span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the lower bound is the (alpha/2)*n-th smallest sample, where n is the</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># number of samples</span></span>
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<pre style="margin: 0;">-<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">lower_bound_indx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">round</span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">alpha</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">num_samples</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="python"> <span class="n" style="color: #333;">lower_bound_indx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">round</span></span><span class="p"><span class="idiff">((</span></span><span class="n" style="color: #333;"><span class="idiff">alpha</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">num_samples</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the upper bound is the (1-alpha/2)*n nth smallest sample, where n is</span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># the number of samples</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">upper_bound_indx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">round</span></span><span class="p"><span class="idiff">((</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">alpha</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff right">num_samples</span></span><span class="p">)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="python"> <span class="n" style="color: #333;">upper_bound_indx</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;"><span class="idiff left">int</span></span><span class="p"><span class="idiff">(</span></span><span class="nb" style="color: #0086b3;"><span class="idiff">round</span></span><span class="p"><span class="idiff">((</span></span><span class="mi" style="color: #099;"><span class="idiff">1</span></span><span class="o" style="font-weight: 600;"><span class="idiff">-</span></span><span class="n" style="color: #333;"><span class="idiff">alpha</span></span><span class="o" style="font-weight: 600;"><span class="idiff">/</span></span><span class="mi" style="color: #099;"><span class="idiff">2</span></span><span class="p"><span class="idiff">)</span></span><span class="o" style="font-weight: 600;"><span class="idiff">*</span></span><span class="n" style="color: #333;"><span class="idiff">num_samples</span></span><span class="p"><span class="idiff right">)</span>)</span> <span class="o" style="font-weight: 600;">-</span> <span class="mi" style="color: #099;">1</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">lower_bound_indx</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="LC51" class="line" lang="python"> <span class="k" style="font-weight: 600;">assert</span><span class="p">(</span><span class="n" style="color: #333;">upper_bound_indx</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="python"> <span class="c1" style="color: #998; font-style: italic;"># sort samples along first axis</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">@@ -168,11 +168,11 @@ def check_gff_and_bam(gff_dir, bam_filename, main_logger,</td>
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<pre style="margin: 0;"> <span id="LC168" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">bam_starts_with_chr</span> <span class="o" style="font-weight: 600;">!=</span> <span class="n" style="color: #333;">gff_starts_with_chr</span><span class="p">:</span></span>
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<pre style="margin: 0;"> <span id="LC169" class="line" lang="python"> <span class="n" style="color: #333;">mismatch_found</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="LC170" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">mismatch_found</span><span class="p">:</span></span>
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<pre style="margin: 0;">-<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">m<span class="idiff left right">iso</span>_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"It looks like your GFF annotation file and your BAM "</span> \</span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="python"> <span class="n" style="color: #333;">m<span class="idiff left right">ain</span>_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"It looks like your GFF annotation file and your BAM "</span> \</span>
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<pre style="margin: 0;"> <span id="LC172" class="line" lang="python"> <span class="s" style="color: #d14;">"file might not have matching headers (chromosome names.) "</span> \</span>
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<pre style="margin: 0;"> <span id="LC173" class="line" lang="python"> <span class="s" style="color: #d14;">"If this is the case, your run will fail as no reads from "</span> \</span>
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="python"> <span class="s" style="color: #d14;">"the BAM could be matched up with your annotation."</span><span class="p">)</span></span>
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<pre style="margin: 0;">-<span id="LC175" class="line" lang="python"> <span class="n" style="color: #333;">m<span class="idiff left right">iso</span>_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Please see:</span><span class="se" style="color: #d14;">\n\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> for more information."</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">manual_url</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="python"> <span class="n" style="color: #333;">m<span class="idiff left right">ain</span>_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Please see:</span><span class="se" style="color: #d14;">\n\t</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s</span><span class="se" style="color: #d14;">\n</span><span class="s" style="color: #d14;"> for more information."</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">manual_url</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># Default: assume BAM starts with chr headers</span></span>
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177
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177
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<pre style="margin: 0;"> <span id="LC177" class="line" lang="python"> <span class="n" style="color: #333;">chr_containing</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"BAM file (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s)"</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">bam_filename</span><span class="p">)</span></span>
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178
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178
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<pre style="margin: 0;"> <span id="LC178" class="line" lang="python"> <span class="n" style="color: #333;">not_chr_containing</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"GFF annotation (</span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s)"</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">gff_dir</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">@@ -180,16 +180,16 @@ def check_gff_and_bam(gff_dir, bam_filename, main_logger,</td>
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180
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180
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<pre style="margin: 0;"> <span id="LC180" class="line" lang="python"> <span class="c1" style="color: #998; font-style: italic;"># BAM does not start with chr, GFF does</span></span>
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181
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<pre style="margin: 0;"> <span id="LC181" class="line" lang="python"> <span class="n" style="color: #333;">chr_containing</span><span class="p">,</span> <span class="n" style="color: #333;">not_chr_containing</span> <span class="o" style="font-weight: 600;">=</span> \</span>
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182
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182
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<pre style="margin: 0;"> <span id="LC182" class="line" lang="python"> <span class="n" style="color: #333;">not_chr_containing</span><span class="p">,</span> <span class="n" style="color: #333;">chr_containing</span></span>
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<pre style="margin: 0;">-<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">m<span class="idiff left right">iso</span>_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"It looks like your </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s contains </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">chr</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;"> chromosomes (UCSC-style) "</span> \</span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="python"> <span class="n" style="color: #333;">m<span class="idiff left right">ain</span>_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"It looks like your </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s contains </span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;">chr</span><span class="se" style="color: #d14;">\'</span><span class="s" style="color: #d14;"> chromosomes (UCSC-style) "</span> \</span>
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184
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="python"> <span class="s" style="color: #d14;">"while your </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s does not."</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;">chr_containing</span><span class="p">,</span></span>
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185
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185
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="python"> <span class="n" style="color: #333;">not_chr_containing</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="python"> <span class="n" style="color: #333;">m<span class="idiff left right">iso</span>_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"The first few BAM chromosomes were: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> \</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="python"> <span class="n" style="color: #333;">m<span class="idiff left right">ain</span>_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"The first few BAM chromosomes were: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> \</span>
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187
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187
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<pre style="margin: 0;"> <span id="LC187" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">bam_chroms</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">())))</span></span>
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188
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188
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"BAM references: "</span></span>
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189
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189
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="n" style="color: #333;">bam_file</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">references</span></span>
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190
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<pre style="margin: 0;">-<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">m<span class="idiff left right">iso</span>_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"The first few GFF chromosomes were: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> \</span>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="python"> <span class="n" style="color: #333;">m<span class="idiff left right">ain</span>_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"The first few GFF chromosomes were: </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s"</span> \</span>
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<pre style="margin: 0;"> <span id="LC191" class="line" lang="python"> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="s" style="color: #d14;">","</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">join</span><span class="p">(</span><span class="n" style="color: #333;">gff_chroms</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">keys</span><span class="p">())))</span></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">m<span class="idiff left right">iso</span>_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Run is likely to fail or produce empty output. Proceeding "</span> \</span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="python"> <span class="n" style="color: #333;">m<span class="idiff left right">ain</span>_logger</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">warning</span><span class="p">(</span><span class="s" style="color: #d14;">"Run is likely to fail or produce empty output. Proceeding "</span> \</span>
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<pre style="margin: 0;"> <span id="LC193" class="line" lang="python"> <span class="s" style="color: #d14;">"anyway..."</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="python"> <span class="n" style="color: #333;">time</span><span class="o" style="font-weight: 600;">.</span><span class="n" style="color: #333;">sleep</span><span class="p">(</span><span class="mi" style="color: #099;">15</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC195" class="line" lang="python"></span>
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<a href="https://salsa.debian.org/med-team/python-misopy/commit/a7cdbd7f99b285512161da0606ad2ca6fdc23820#db070d7c8c5a7d9163c5110129e29cd6f14df2ed"><strong>misopy/samples_utils.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">@@ -303,7 +303,7 @@ def summarize_sampler_results(samples_dir, summary_filename,</td>
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<pre style="margin: 0;"> <span id="LC303" class="line" lang="python"> <span class="n" style="color: #333;">counts_info</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">samples_results</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="LC304" class="line" lang="python"> <span class="n" style="color: #333;">shape_len</span> <span class="o" style="font-weight: 600;">=</span> <span class="nb" style="color: #0086b3;">len</span><span class="p">(</span><span class="n" style="color: #333;">shape</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">))</span></span>
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<pre style="margin: 0;"> <span id="LC305" class="line" lang="python"> <span class="k" style="font-weight: 600;">if</span> <span class="n" style="color: #333;">shape_len</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="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"WARNING: Skipping </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s -- mishaped file"</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">samples_file</span>name</span><span class="p">)</span></span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="python"> <span class="k" style="font-weight: 600;">print</span> <span class="s" style="color: #d14;">"WARNING: Skipping </span><span class="si" style="color: #d14;">%</span><span class="s" style="color: #d14;">s -- mishaped file"</span> <span class="o" style="font-weight: 600;">%</span><span class="p">(</span><span class="n" style="color: #333;"><span class="idiff left right">event_</span>name</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC307" class="line" lang="python"> <span class="k" style="font-weight: 600;">continue</span></span>
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<pre style="margin: 0;"> <span id="LC308" class="line" lang="python"> <span class="n" style="color: #333;">num_samples</span><span class="p">,</span> <span class="n" style="color: #333;">num_isoforms</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">shape</span><span class="p">(</span><span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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<pre style="margin: 0;"> <span id="LC309" class="line" lang="python"> <span class="n" style="color: #333;">output_fields</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">format_credible_intervals</span><span class="p">(</span><span class="n" style="color: #333;">event_name</span><span class="p">,</span> <span class="n" style="color: #333;">samples</span><span class="p">)</span></span>
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<a href="https://salsa.debian.org/med-team/python-misopy/commit/a7cdbd7f99b285512161da0606ad2ca6fdc23820#84d5450da339c483f205f0e34adc7fca5353997c"><strong>pysplicing/src/miso.c</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="365" 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="365" 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">@@ -365,7 +365,6 @@ int splicing_drift_proposal_init(int noiso, int noChains,</td>
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<pre style="margin: 0;"> <span id="LC365" class="line" lang="c"> <span class="n" style="color: #333;">MATRIX</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">respsi</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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="n" style="color: #333;">RNG_UNIF01</span><span class="p">();</span></span>
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<pre style="margin: 0;"> <span id="LC366" class="line" lang="c"> <span class="n" style="color: #333;">MATRIX</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">respsi</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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;">1</span> <span class="o" style="font-weight: 600;">-</span> <span class="n" style="color: #333;">MATRIX</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">respsi</span><span class="p">,</span> <span class="n" style="color: #333;">j</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="LC367" class="line" lang="c"> <span class="n" style="color: #333;">MATRIX</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">resalpha</span><span class="p">,</span> <span class="mi" style="color: #099;">0</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 class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;">-<span id="LC368" class="line" lang="c"> <span class="n" style="color: #333;">MATRIX</span><span class="p">(</span><span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">resalpha</span><span class="p">,</span> <span class="mi" style="color: #099;">1</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 class="mi" style="color: #099;">0</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC368" class="line" lang="c"> <span class="p">}</span></span>
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<pre style="margin: 0;"> <span id="LC369" class="line" lang="c"> <span class="o" style="font-weight: 600;">*</span><span class="n" style="color: #333;">ressigma</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">SIGMA</span><span class="p">;</span></span>
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<pre style="margin: 0;"> <span id="LC370" class="line" lang="c"> <span class="p">}</span></span>
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<a href="https://salsa.debian.org/med-team/python-misopy/commit/a7cdbd7f99b285512161da0606ad2ca6fdc23820#8c91c0296909b5ea3c496fde69e9dc44a6c6ae5f"><strong>setup.cfg</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">[egg_info]</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">tag_build = </span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">tag_date = 0</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">tag_svn_revision = 0</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"></span></pre>
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<a href="https://salsa.debian.org/med-team/python-misopy/commit/a7cdbd7f99b285512161da0606ad2ca6fdc23820#8e2edce0d507e1297474f25c00cae94258db38d8"><strong>setup.py</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;"><span class="idiff left right">distutils.core</span></span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span><span class="p">,</span> <span class="n" style="color: #333;">Extension</span></span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="python"><span class="kn" style="font-weight: 600;">from</span> <span class="nn" style="color: #555;"><span class="idiff left right">setuptools</span></span> <span class="kn" style="font-weight: 600;">import</span> <span class="n" style="color: #333;">setup</span><span class="p">,</span> <span class="n" style="color: #333;">Extension</span></span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">distutils.ccompiler</span></span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="python"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">glob</span></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;">os</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">@@ -74,7 +74,7 @@ for scheme in INSTALL_SCHEMES.values():</td>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">## Definition of the current version. This is defined here</span></span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">## and then gets written to __init__.py in misopy.</span></span>
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<pre style="margin: 0;"> <span id="LC76" class="line" lang="python"><span class="c1" style="color: #998; font-style: italic;">##</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="python"><span class="n" style="color: #333;">MISO_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.5.<span class="idiff left right">3</span>"</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="python"><span class="n" style="color: #333;">MISO_VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"0.5.<span class="idiff left right">4</span>"</span></span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="python"></span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="python"><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="python"><span class="c1" style="color: #998; font-style: italic;">## Generate a __version__.py attribute</span></span>
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