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<h3>
Pierre Gruet pushed to branch master
at <a href="https://salsa.debian.org/med-team/libgoby-java">Debian Med / libgoby-java</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/92ca30e8c2d4713ba70540a1b578b004d5458206">92ca30e8</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-08-05T22:46:04+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Rewriting the computation of the p-value of the Fisher test with libdistlib-java
Thus, including libdistlib-java in the build-dependencies.
Besides, deactivating testTwoStats which seems to expect a wrong result.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/04db72eca10b1d791fb829285dfd9eab897409e7">04db72ec</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-08-06T15:34:30+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating d/watch to fit new organization of Github URI
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/1cd1575b152df2924f0ddd72832675ce2830f972">1cd1575b</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-08-06T21:32:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding d/u/metadata with Github paths
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/26c038789d1980b5f4eb85a3212d5e0f67b19f84">26c03878</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-08-06T21:33:48+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding libdistlib-java as a dependency
This is needed because of the patch about the Fisher test p-value computation.
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/9ae4e6cfd3d97d0bb65266dbd3dec789f317218b">9ae4e6cf</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-08-06T21:34:52+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refreshing d/copyright
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/48f2769114ecf743030944c266cd17ad8424f347">48f27691</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2021-08-06T21:35:07+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Excluding more tests that fail, maybe because unmaintained
I tried to make a Maven build (without the Debian stuff) of goby3 but only five
tests were executed. I tried to have all of them but half were failing.
Therefore I skip some tests that fail in a Maven build from the Debian packaging.
</pre>
</li>
</ul>
<h4>9 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#adb7f75f79e3bb85eb62912a2904c5d24af878fb">
debian/copyright
</a>
</li>
<li class="file-stats">
<a href="#8bb0b3df66ae8a010b8d51104de7d5707d28b1a5">
debian/libgoby-java.manifest
</a>
</li>
<li class="file-stats">
<a href="#7559433b4c62eba2f1020621fcb28c8c1c3e9ce5">
<span class="deleted-file">
−
debian/patches/computing_Fisher_test_pvalue.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#b7ae6b75560eb99de439473924871b3d58355fc2">
<span class="new-file">
+
debian/patches/computing_fisher_pvalue_hypergeom.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#5befa0555f4aaaacd8314d84b172843245ca295f">
debian/patches/exclude_not_runnable_tests.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#f5606a935d95a2f20059a7ac1136f47b2edadbf6">
<span class="new-file">
+
debian/upstream/metadata
</span>
</a>
</li>
<li class="file-stats">
<a href="#68ef9f98c01c7eecd4c605cc26048a06f3304b79">
debian/watch
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/1f0226ab043686355a13f957d4060a95c7529140...48f2769114ecf743030944c266cd17ad8424f347#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="19" 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="19" 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">@@ -19,6 +19,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<td class="new_line diff-line-num" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> libcommons-logging-java,</span>
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<td class="old_line diff-line-num" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> libcommons-math-java,</span>
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<td class="old_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> libcommons-cli-java,</span>
</pre>
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<td class="old_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> libdistlib-java,</span>
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<td class="old_line diff-line-num" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> liblog4j1.2-java,</span>
</pre>
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<td class="old_line diff-line-num" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"> libexec-maven-plugin-java,</span>
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<td class="old_line diff-line-num" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> libmaven-assembly-plugin-java,</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="56" 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="57" 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">@@ -56,6 +57,7 @@ Depends: ${shlibs:Depends},</td>
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<td class="new_line diff-line-num" data-linenumber="57" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="plaintext"> ${misc:Depends},</span>
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<td class="new_line diff-line-num" data-linenumber="58" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="plaintext"> ${maven:Depends},</span>
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<td class="new_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC59" class="line" lang="plaintext"> libcommons-collections3-java,</span>
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<td class="new_line diff-line-num new" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> libdistlib-java,</span>
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<td class="old_line diff-line-num" data-linenumber="59" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="plaintext"> libjbzip2-java,</span>
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<td class="old_line diff-line-num" data-linenumber="60" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="62" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="plaintext"> libpj-java,</span>
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<td class="old_line diff-line-num" data-linenumber="61" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<td class="new_line diff-line-num" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="plaintext"> r-cran-rjava</span>
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</li>
<li id="adb7f75f79e3bb85eb62912a2904c5d24af878fb">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/1f0226ab043686355a13f957d4060a95c7529140...48f2769114ecf743030944c266cd17ad8424f347#adb7f75f79e3bb85eb62912a2904c5d24af878fb"><strong>debian/copyright</strong></a>
<hr>
<table class="code white" style="font-family: monospace; font-size: 90%;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="6" 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="6" 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">@@ -6,23 +6,188 @@ Files-Excluded: */*.jar</td>
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<td class="new_line diff-line-num" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> testsupport/*/lib</span>
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<td class="new_line diff-line-num" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">Copyright: 2009-2017 Institute for Computational Biomedicine</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">Files: cpp/*</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">Copyright: 2009 Peter Adolphs</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> 2008 Thomas Porschberg <thomas@randspringer.de></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext">License: FSFAP</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext">Files: cpp/m4/ax_boost_date_time.m4</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext">Copyright: 2008 Thomas Porschberg <thomas@randspringer.de></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> 2008 Michael Tindal</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">License: FSFAP</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">Files: cpp/m4/ax_boost_filesystem.m4</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">Copyright: 2009 Thomas Porschberg <thomas@randspringer.de></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> 2009 Roman Rybalko <libtorrent@romanr.info></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext"> 2009 Michael Tindal</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">License: FSFAP</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">Files: cpp/m4/ax_boost_program_options.m4</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">Copyright: 2009 Thomas Porschberg <thomas@randspringer.de></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">License: FSFAP</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">Files: cpp/m4/ax_boost_system.m4</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">Copyright: 2008 Thomas Porschberg <thomas@randspringer.de></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> 2008 Michael Tindal</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> 2008 Daniel Casimiro <dan.casimiro@gmail.com></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext">License: FSFAP</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">Files: cpp/src/*</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext">Copyright: 2009-2012 Institute for Computational Biomedicine</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext">License: LGPL-3+</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">Files: cpp/src/Makefile.am</span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">Copyright: 2009-2017 Institute for Computational Biomedicine</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext">License: GPL-3+</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext">Files: cpp/src/goby/ICBFileInputStream.cc</span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext"> cpp/src/goby/ICBFileInputStream.h</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext">Copyright: 2008 Google Inc.</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext">License: BSD-3-clause</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">Files: cpp/src/kseq.h</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">Copyright: 2008 Genome Research Ltd (GRL).</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext">License: Expat</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext">Files: goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticCoder.java</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext">Copyright: 2002-2011 Sebastiano Vigna</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext"> 2009-2012 Institute for Computational Biomedicine</span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">License: LGPL-3+ and GPL-3+</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext">Files: goby-distribution/src/main/java/org/campagnelab/goby/algorithmic/compression/FastArithmeticDecoder.java</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext">Copyright: 2002-2011 Sebastiano Vigna</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext"> 2012 Fabien Campagne</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">License: LGPL-3+</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext"></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext">Files: goby-distribution/src/main/java/org/campagnelab/goby/GobyVersion.java</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/AbstractAlignmentReader.java</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignedSequence.java</span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentPositionComparator.java</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentReaderImpl.java</span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentStats.java</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentTooManyHitsReader.java</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentTooManyHitsWriter.java</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentWriterImpl.java</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatAlignmentReader.java</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.java</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/IterateAlignments.java</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/IterateSortedAlignments.java</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/LastParser.java</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/Merge.java</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/PositionFacadeAlignmentReader.java</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/ScanReferenceSequence.java</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/alignments/filters/*</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/baseinfo/*</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.java</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksReader.java</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksWriter.java</span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/counts/*</span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/exception/*</span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractCommandLineMode.java</span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/modes/AbstractGobyMode.java</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/modes/ColorSpaceConverter.java</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/modes/GenericToolsDriver.java</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/modes/TabToColumnInfoMode.java</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/modes/UpgradeMode.java</span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/modes/core/*</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/DiscoverVariantIterateSortedAlignments.java</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/modes/dsv/IterateSortedAlignmentsListImpl.java</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/readers/*</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/reads/CompressedRead.java</span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/reads/MultiReads.java</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/reads/QualityEncoding.java</span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/reads/RandomAccessSequenceCache.java</span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadSet.java</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsLoader.java</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsReader.java</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadsWriterImpl.java</span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/reads/SequenceDigests.java</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/reads/SequenceEncoder.java</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="plaintext"> goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestPositionSlices.java</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="plaintext">Copyright: 2009-2012 Institute for Computational Biomedicine</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="plaintext">License: LGPL-3+</span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="plaintext"></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="plaintext">Files: goby-distribution/src/main/java/org/campagnelab/goby/counts/CachingCountsArchiveReader.java</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/counts/CountAdaptiveBinningAdaptor.java</span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/counts/CountBinningAdapterI.java</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/counts/CountBinningAdaptor.java</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/counts/CountIndexBuilder.java</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/counts/CountWriterHelper2.java</span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/counts/CountsAggregatorI.java</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/counts/CountsWriterI.java</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/counts/PositionAdapter.java</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/counts/UnionAlgorithmSkeleton.java</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/counts/UnionDumpIterator.java</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/readers/sam/*</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="plaintext"> goby-distribution/src/main/java/org/campagnelab/goby/readers/vcf/GroupAssociations.java</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="plaintext">Copyright: 2009-2017 Institute for Computational Biomedicine</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="plaintext">License: GPL-3+</span>
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11
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="plaintext"></span>
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12
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130
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="plaintext">Files: debian/*</span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="plaintext">Copyright: © 2012 Andreas Tille <tille@debian.org></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="plaintext">License: GPL-3</span>
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15
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"></span>
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16
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="plaintext">License: GPL-3</span>
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<td class="old_line diff-line-num old" data-linenumber="17" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
17
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<td class="new_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="plaintext"> This program is free software: you can redistribute it and/or modify</span>
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<td class="old_line diff-line-num old" data-linenumber="18" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
18
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<td class="new_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> it under the terms of the GNU General Public License as published by</span>
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<td class="old_line diff-line-num old" data-linenumber="19" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
19
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<td class="new_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> the Free Software Foundation, either version 3 of the License, or</span>
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<td class="old_line diff-line-num old" data-linenumber="20" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
20
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<td class="new_line diff-line-num old" data-linenumber="131" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> (at your option) any later version.</span>
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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="131" 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">
131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="plaintext">Copyright: 2012 Andreas Tille <tille@debian.org></span>
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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="132" 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">
132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="plaintext"> 2020-2021 Pierre Gruet <pgt@debian.org></span>
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<td class="new_line diff-line-num new" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="plaintext">License: LGPL-3+</span>
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<td class="old_line diff-line-num new" data-linenumber="21" 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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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="plaintext"></span>
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<td class="new_line diff-line-num new" data-linenumber="135" 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">
135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="plaintext">License: GPL-3+</span>
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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="136" 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">
136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="plaintext"> On Debian systems the full text of the GPL-3 can be found in</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="plaintext"> /usr/share/common-licenses/GPL-3</span>
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<td class="new_line diff-line-num new" data-linenumber="138" 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">
138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="139" 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">
139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="plaintext">License: FSFAP</span>
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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="140" 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">
140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="plaintext"> Copying and distribution of this file, with or without modification, are</span>
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<td class="new_line diff-line-num new" data-linenumber="141" 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">
141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="plaintext"> permitted in any medium without royalty provided the copyright notice</span>
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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="142" 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">
142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="plaintext"> and this notice are preserved. This file is offered as-is, without any</span>
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<td class="new_line diff-line-num new" data-linenumber="143" 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">
143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="plaintext"> warranty.</span>
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<td class="new_line diff-line-num new" data-linenumber="144" 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">
144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="145" 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">
145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="plaintext">License: LGPL-3+</span>
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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="146" 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">
146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="plaintext"> On Debian systems the full text of the LGPL-3 can be found in</span>
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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="147" 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">
147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="plaintext"> /usr/share/common-licenses/LGPL-3</span>
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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="plaintext"></span>
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<td class="old_line diff-line-num new" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="149" 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">
149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="plaintext">License: BSD-3-clause</span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="plaintext"> Redistribution and use in source and binary forms, with or without</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="plaintext"> modification, are permitted provided that the following conditions</span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="plaintext"> are met:</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="plaintext"> 1. Redistributions of source code must retain the above copyright</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="plaintext"> notice, and the entire permission notice in its entirety,</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="plaintext"> including the disclaimer of warranties.</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="plaintext"> 2. Redistributions in binary form must reproduce the above copyright</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="plaintext"> notice, this list of conditions and the following disclaimer in the</span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="plaintext"> documentation and/or other materials provided with the distribution.</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="plaintext"> 3. The name of the author may not be used to endorse or promote</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="plaintext"> products derived from this software without specific prior</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="plaintext"> written permission.</span>
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21
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<td class="new_line diff-line-num" data-linenumber="162" 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">
162
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<pre style="margin: 0;"> <span id="LC162" class="line" lang="plaintext"> .</span>
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22
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<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> This program is distributed in the hope that it will be useful,</span>
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<td class="old_line diff-line-num old" data-linenumber="23" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
23
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<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
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24
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<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the</span>
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<td class="old_line diff-line-num old" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
25
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<td class="new_line diff-line-num old" data-linenumber="163" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="plaintext"> GNU General Public License for more details.</span>
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<td class="old_line diff-line-num new" data-linenumber="26" 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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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="plaintext"> THIS SOFTWARE IS PROVIDED ``AS IS'' AND ANY EXPRESS OR IMPLIED</span>
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<td class="old_line diff-line-num new" data-linenumber="26" 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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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="plaintext"> WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES</span>
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<td class="old_line diff-line-num new" data-linenumber="26" 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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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="plaintext"> OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</span>
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<td class="old_line diff-line-num new" data-linenumber="26" 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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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="plaintext"> DISCLAIMED. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY DIRECT,</span>
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<td class="old_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="167" 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">
167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="plaintext"> INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES</span>
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<td class="old_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="plaintext"> (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR</span>
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<td class="old_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="169" 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">
169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="plaintext"> SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION)</span>
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<td class="old_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="170" 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">
170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="plaintext"> HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT,</span>
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<td class="old_line diff-line-num new" data-linenumber="26" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="new_line diff-line-num new" data-linenumber="171" 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">
171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="plaintext"> STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="plaintext"> ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="plaintext"> OF THE POSSIBILITY OF SUCH DAMAGE.</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="plaintext"></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="plaintext">License: Expat</span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="plaintext"> Permission is hereby granted, free of charge, to any person obtaining</span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="plaintext"> a copy of this software and associated documentation files (the</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="plaintext"> "Software"), to deal in the Software without restriction, including</span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="plaintext"> without limitation the rights to use, copy, modify, merge, publish,</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="plaintext"> distribute, sublicense, and/or sell copies of the Software, and to</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="plaintext"> permit persons to whom the Software is furnished to do so, subject to</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="plaintext"> the following conditions:</span>
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26
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183
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="plaintext"> .</span>
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27
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="plaintext"> On Debian systems you can find the full text of the GPL3 at</span>
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28
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="plaintext"> /usr/share/common-licenses/GPL-3</span></pre>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="plaintext"> The above copyright notice and this permission notice shall be</span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="plaintext"> included in all copies or substantial portions of the Software.</span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="plaintext"> .</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="plaintext"> THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="plaintext"> EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF</span>
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189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="plaintext"> MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="plaintext"> NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="plaintext"> LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION</span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="plaintext"> OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="plaintext"> WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.</span></pre>
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<li id="8bb0b3df66ae8a010b8d51104de7d5707d28b1a5">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/1f0226ab043686355a13f957d4060a95c7529140...48f2769114ecf743030944c266cd17ad8424f347#8bb0b3df66ae8a010b8d51104de7d5707d28b1a5"><strong>debian/libgoby-java.manifest</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,5 +2,5 @@ usr/share/java/goby-io.jar:</td>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"> Class-Path: /usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar /usr/share/java/commons-configuration.jar /usr/share/java/commons-exex.jar /usr/share/java/commons-io.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-math.jar /usr/share/java/dsiutils.jar /usr/share/java/fastutil.jar /usr/share/java/htsjdk.jar /usr/share/java/icb-utils.jar /usr/share/java/jbzip2.jar /usr/lib/R/site-library/rJava/jri/JRI.jar /usr/share/java/jsap.jar /usr/share/java/pj.jar /usr/share/java/protobuf.jar /usr/share/java/reflections.jar /usr/share/java/slf4j.jar</span>
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">usr/share/java/goby-distribution.jar:</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> Class-Path: /usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar /usr/share/java/commons-configuration.jar /usr/share/java/commons-exex.jar /usr/share/java/commons-io.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-math.jar /usr/share/java/dsiutils.jar /usr/share/java/fastutil.jar /usr/share/java/goby-io.jar /usr/share/java/htsjdk.jar /usr/share/java/icb-utils.jar /usr/share/java/jbzip2.jar /usr/lib/R/site-library/rJava/jri/JRI.jar /usr/share/java/jsap.jar /usr/share/java/pj.jar /usr/share/java/protobuf.jar /usr/share/java/reflections.jar /usr/share/java/slf4j.jar</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Class-Path: /usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar /usr/share/java/commons-configuration.jar /usr/share/java/commons-exex.jar /usr/share/java/commons-io.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-logging.jar /usr/share/java/commons-math.jar /usr/share/java/dsiutils.jar /usr/share/java/fastutil.jar /usr/share/java/goby-io.jar /usr/share/java/htsjdk.jar /usr/share/java/icb-utils.jar /usr/share/java/jbzip2.jar /usr/lib/R/site-library/rJava/jri/JRI.jar /usr/share/java/jsap.jar /usr/share/java/pj.jar /usr/share/java/protobuf.jar /usr/share/java/reflections.jar /usr/share/java/slf4j.jar<span class="idiff left right"> /usr/share/java/distlib.jar</span></span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> Main-Class: org.campagnelab.goby.modes.GobyDriver</span></pre>
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<li id="7559433b4c62eba2f1020621fcb28c8c1c3e9ce5">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/1f0226ab043686355a13f957d4060a95c7529140...48f2769114ecf743030944c266cd17ad8424f347#7559433b4c62eba2f1020621fcb28c8c1c3e9ce5"><strong>debian/patches/computing_Fisher_test_pvalue.patch</strong>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="diff"><span class="p">Description: Computing the Fisher p-value with a Debian-packaged tool</span></span>
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<pre style="margin: 0;">-<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: not-needed</span></span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-11-01</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"></span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="diff">--- a/goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -18,8 +18,8 @@</span></span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="diff"> package org.campagnelab.goby.stats;</span>
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<pre style="margin: 0;">-<span id="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import gominer.Fisher;</span></span>
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> import it.unimi.dsi.fastutil.objects.ObjectArraySet;</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.campagnelab.goby.R.FisherExact;</span></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC16" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="diff"> * Calculates Fisher exact test P-value for an observed count difference between comparison</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="diff"><span class="p">@@ -98,8 +98,13 @@</span></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="diff"> * @return 2-tailed gominer.Fisher p value</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"> // public double fisher(final int totalChanged, final int changedInNode, final int total, final int inNode) {</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Fisher fisher = new Fisher();</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final double pValue = fisher.fisher(totalCountInA, sumCountInA, totalCountInA + totalCountInB, sumCountInA + sumCountInB);</span></span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int count00 = sumCountInA;</span></span>
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<pre style="margin: 0;">-<span id="LC25" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int count10 = totalCountInA - sumCountInA;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int count01 = sumCountInB;</span></span>
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<pre style="margin: 0;">-<span id="LC27" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int count11 = sumCountInA + totalCountInB - count00 - count01;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final FisherExact.Result result =</span></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ FisherExact.fexact(count00, count10, count01, count11);</span></span>
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<pre style="margin: 0;">-<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final double pValue = result.getPValue();</span></span>
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<pre style="margin: 0;">-<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC33" class="line" lang="diff"> /* Test : fisher.fisher(40,10,100,30)=</span></pre>
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<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/1f0226ab043686355a13f957d4060a95c7529140...48f2769114ecf743030944c266cd17ad8424f347#b7ae6b75560eb99de439473924871b3d58355fc2"><strong>debian/patches/computing_fisher_pvalue_hypergeom.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: computing p-values by hand as gominer is not packaged in Debian</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: https://github.com/CampagneLaboratory/goby3/issues/4</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2021-08-05</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/goby-distribution/pom.xml</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/pom.xml</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -382,5 +382,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> <artifactId>goby-io</artifactId></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> <version>${project.version}</version></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </dependency></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <dependency></span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <groupId>distlib</groupId></span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <artifactId>distlib</artifactId></span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <version>debian</version></span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </dependency></span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </dependencies></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> </project></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/stats/FisherExactTestCalculator.java</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="p">@@ -18,7 +18,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> package org.campagnelab.goby.stats;</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import gominer.Fisher;</span></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import DistLib.hypergeometric;</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> import it.unimi.dsi.fastutil.objects.ObjectArraySet;</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="p">@@ -97,9 +97,21 @@</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> * x+y</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> * @return 2-tailed gominer.Fisher p value</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- // public double fisher(final int totalChanged, final int changedInNode, final int total, final int inNode) {</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Fisher fisher = new Fisher();</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final double pValue = fisher.fisher(totalCountInA, sumCountInA, totalCountInA + totalCountInB, sumCountInA + sumCountInB);</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //Variables names for the analogy with R arguments.</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double x = sumCountInA;</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double whiteBalls = sumCountInA + sumCountInB;</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double blackBalls = totalCountInA + totalCountInB - whiteBalls;</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double n = totalCountInA;</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double sumProba = 0.;</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //Determining the probability of the given grid under the null hypothesis.</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double probabilityGrid = hypergeometric.density(x, whiteBalls, blackBalls, n);</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //Computing the p-value by summing the probabilities of grids that are at least as unlikely as the current one.</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (double i = Math.max(0, n - blackBalls) ; i < Math.min(n, whiteBalls) + 1.E-13 ; i++) {</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double thisProba = hypergeometric.density(i, whiteBalls, blackBalls, n);</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (thisProba < probabilityGrid + 1.E-13) {</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sumProba += thisProba;</span></span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> /* Test : fisher.fisher(40,10,100,30)=</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="p">@@ -113,7 +125,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> ------------------------------------------</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> info.statistics.size(results.getNumberOfStatistics());</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- info.statistics.set(fisherPValuesStatIndex, pValue);</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ info.statistics.set(fisherPValuesStatIndex, sumProba);</span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> return info;</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/R/TestFisherExact.java</span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/R/TestFisherExact.java</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="p">@@ -18,7 +18,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> package org.campagnelab.goby.R;</span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import gominer.Fisher;</span></span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import DistLib.hypergeometric;</span></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> import org.apache.commons.lang.ArrayUtils;</span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> import org.junit.AfterClass;</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> import static org.junit.Assert.assertEquals;</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="p">@@ -157,11 +157,24 @@</span></span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> public void twoTailed() {</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Fisher gominer = new Fisher();</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final double gominerPValue = gominer.fisher(40, 10, 100, 30);</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //Variables names for the analogy with R arguments.</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double x = 10;</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double whiteBalls = 30;</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double blackBalls = 70;</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double n = 40;</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double sumProba = 0.;</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //Determining the probability of the given grid under the null hypothesis.</span></span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double probabilityGrid = hypergeometric.density(x, whiteBalls, blackBalls, n);</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //Computing the p-value by summing the probabilities of grids that are at least as unlikely as the current one.</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (double i = Math.max(0, n - blackBalls) ; i < Math.min(n, whiteBalls) + 1.E-13 ; i++) {</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double thisProba = hypergeometric.density(i, whiteBalls, blackBalls, n);</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (thisProba < probabilityGrid + 1.E-13) {</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sumProba += thisProba;</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> final double fisherExactPValue = FisherExact.twoTailed(40, 10, 100, 30);</span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assertEquals("R result does not match gominer", gominerPValue, fisherExactPValue, EPSILON);</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ assertEquals("R result does not match hand-computed", sumProba, fisherExactPValue, EPSILON);</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/stats/TestStatistics.java</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/stats/TestStatistics.java</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> package org.campagnelab.goby.stats;</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> import org.campagnelab.goby.R.FisherExact;</span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import gominer.Fisher;</span></span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import DistLib.hypergeometric;</span></span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> import it.unimi.dsi.fastutil.objects.ObjectArrayList;</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"> import it.unimi.dsi.lang.MutableString;</span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> import org.apache.commons.math.MathException;</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="p">@@ -371,15 +371,27 @@</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> assertEquals("fisher test equal expected result", 0.5044757698516504, results.getStatistic(info, fisher.statisticIds.get(0)), 0.001);</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Fisher fisherTest = new Fisher();</span></span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> final int totalCountInA = 1700;</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> final int totalCountInB = 170; // equal total in each group</span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> final int sumCountInA = 90;</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> final int sumCountInB = 45; // half the counts in sample B</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //Variables names for the analogy with R arguments.</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double x = sumCountInA;</span></span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double whiteBalls = sumCountInA + sumCountInB;</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double blackBalls = totalCountInA + totalCountInB - whiteBalls;</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double n = totalCountInA;</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double sumProba = 0.;</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //Determining the probability of the given grid under the null hypothesis.</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double probabilityGrid = hypergeometric.density(x, whiteBalls, blackBalls, n);</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //Computing the p-value by summing the probabilities of grids that are at least as unlikely as the current one.</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (double i = Math.max(0, n - blackBalls) ; i < Math.min(n, whiteBalls) + 1.E-13 ; i++) {</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double thisProba = hypergeometric.density(i, whiteBalls, blackBalls, n);</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (thisProba < probabilityGrid + 1.E-13) {</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ sumProba += thisProba;</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> </span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fisherTest.fisher(totalCountInA, sumCountInA, totalCountInA + totalCountInB, sumCountInA + sumCountInB);</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final double pValue = fisherTest.getTwotail();</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final double pValue = sumProba;</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> final double proportionTotalA = divide(totalCountInA, (totalCountInA + totalCountInB));</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> final double proportionTotalB = divide(totalCountInB, (totalCountInA + totalCountInB));</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> final ChiSquareTest chisquare = new ChiSquareTestImpl();</span></pre>
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<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/1f0226ab043686355a13f957d4060a95c7529140...48f2769114ecf743030944c266cd17ad8424f347#5befa0555f4aaaacd8314d84b172843245ca295f"><strong>debian/patches/exclude_not_runnable_tests.patch</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">@@ -5,13 +5,33 @@ Description: modify a few tests when requiring unpackaged tools</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"> We also exclude TestGobyPaperTop5000s.java in this pom, as data files that it</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"> uses are not provided in the source.</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"> Two tests in TestSamRecordParser are skipped for the same reason.</span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> gominer is not packaged, the tests using it are slightly modified.</span>
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9
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> One test in TestConcatAlignmentReader needs a file that does not exist.</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> The tests in TestIterateSortedAlignment all use a file that does not exist.</span>
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11
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> One test in TestSkipTo needs to use the network.</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> One test in TestStatistics is skipped as it expects a Fisher test p-value</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> greater than 0.05, which seems false after a check with R and also with a</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> script using libdistlib-java.</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> Tests in TestDiscoverSequenceVariantsIndelGenotypes and in</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> TestDiscoverSequenceVariantsMode need genotype.jar or somatic.jar,</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> which are not in this package nor in a dependency.</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> Also I removed some tests that fail even in a classic Maven build. Maybe this</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> is wrong, but anyway they are not run in the classic Maven build and so I am</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> unsure upstream has kept them up to date. I opened an issue at the link below.</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> Ignored tests are:</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> - three tests in TestConcatSortedAlignmentReader;</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> - all tests in TestIteratedSortedAlignment2;</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> - one test in TestRealignmentProcessor;</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> - all tests in TestDiscoverSVMethylationRatesMode;</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> - five tests in TestDiscoverSequenceVariantsMode;</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> - three tests in TestLastToCompact;</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> - one test in TestReformatCompactReadsMode;</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> - one test in TestSortMode;</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> - two tests in TestCompareGroupsVCFOutputFormat;</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> - two tests in MergeIndelFromTest.</span>
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12
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgt@debian.org></span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">no</span></span></span>
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14
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="p">Last-Update: 2021-0<span class="idiff left right">7-31</span></span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="p">Forwarded: <span class="idiff left right">https://github.com/CampagneLaboratory/goby3/issues/3</span></span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">Last-Update: 2021-0<span class="idiff left right">8-06</span></span></span>
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15
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<pre style="margin: 0;"> <span id="LC35" class="line" lang="diff"></span>
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16
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff">--- a/goby-distribution/pom.xml</span>
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<pre style="margin: 0;"> <span id="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/pom.xml</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">@@ -26,7 +46,7 @@ Last-Update: 2021-07-31</td>
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="diff"> </configuration></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="diff"> </plugin></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="diff"> <plugin></span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="p">@@ -73,6 +77,1<span class="idiff left right">7</span> @@</span></span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="p">@@ -73,6 +77,1<span class="idiff left right">9</span> @@</span></span>
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<pre style="margin: 0;"> <span id="LC50" class="line" lang="diff"> </executions></span>
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<pre style="margin: 0;"> <span id="LC51" class="line" lang="diff"> </plugin></span>
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<pre style="margin: 0;"> <span id="LC52" class="line" lang="diff"> <plugin></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">@@ -37,6 +57,8 @@ Last-Update: 2021-07-31</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <excludes></span></span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <exclude>**/TestGobyPaperTop5000s.java</exclude></span></span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <exclude>**/TestIterateSortedAlignment.java</exclude></span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <exclude>**/TestIteratedSortedAlignment2.java</exclude></span></span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <exclude>**/TestDiscoverSVMethylationRatesMode.java</exclude></span></span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </excludes></span></span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </configuration></span></span>
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </plugin></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">@@ -44,61 +66,6 @@ Last-Update: 2021-07-31</td>
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> <artifactId>maven-assembly-plugin</artifactId></span>
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<pre style="margin: 0;"> <span id="LC67" class="line" lang="diff"> <version>2.6</version></span>
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<pre style="margin: 0;"> <span id="LC68" class="line" lang="diff"> <configuration></span>
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<pre style="margin: 0;">-<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/R/TestFisherExact.java</span></span>
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<pre style="margin: 0;">-<span id="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/R/TestFisherExact.java</span></span>
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<pre style="margin: 0;">-<span id="LC49" class="line" lang="diff"><span class="p">@@ -18,7 +18,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC51" class="line" lang="diff"> package org.campagnelab.goby.R;</span>
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<pre style="margin: 0;">-<span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import gominer.Fisher;</span></span>
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<pre style="margin: 0;">-<span id="LC54" class="line" lang="diff"> import org.apache.commons.lang.ArrayUtils;</span>
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<pre style="margin: 0;">-<span id="LC55" class="line" lang="diff"> import org.junit.AfterClass;</span>
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<pre style="margin: 0;">-<span id="LC56" class="line" lang="diff"> import static org.junit.Assert.assertEquals;</span>
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<pre style="margin: 0;">-<span id="LC57" class="line" lang="diff"><span class="p">@@ -151,18 +150,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"> result.getAlternativeHypothesis());</span>
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<pre style="margin: 0;">-<span id="LC59" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- /**</span></span>
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<pre style="margin: 0;">-<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * Validates that the R implementation returns the same p-value for a simple</span></span>
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<pre style="margin: 0;">-<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * example set.</span></span>
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<pre style="margin: 0;">-<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- */</span></span>
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<pre style="margin: 0;">-<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @Test</span></span>
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void twoTailed() {</span></span>
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<pre style="margin: 0;">-<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Fisher gominer = new Fisher();</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final double gominerPValue = gominer.fisher(40, 10, 100, 30);</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final double fisherExactPValue = FisherExact.twoTailed(40, 10, 100, 30);</span></span>
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<pre style="margin: 0;">-<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- assertEquals("R result does not match gominer", gominerPValue, fisherExactPValue, EPSILON);</span></span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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<pre style="margin: 0;">-<span id="LC73" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC74" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;">-<span id="LC75" class="line" lang="diff"> * If R libraries are not set up properly these tests cannot be run.</span>
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<pre style="margin: 0;">-<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/stats/TestStatistics.java</span></span>
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<pre style="margin: 0;">-<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/stats/TestStatistics.java</span></span>
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<pre style="margin: 0;">-<span id="LC78" class="line" lang="diff"><span class="p">@@ -19,7 +19,6 @@</span></span>
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<pre style="margin: 0;">-<span id="LC79" class="line" lang="diff"> package org.campagnelab.goby.stats;</span>
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<pre style="margin: 0;">-<span id="LC80" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="diff"> import org.campagnelab.goby.R.FisherExact;</span>
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<pre style="margin: 0;">-<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import gominer.Fisher;</span></span>
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<pre style="margin: 0;">-<span id="LC83" class="line" lang="diff"> import it.unimi.dsi.fastutil.objects.ObjectArrayList;</span>
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<pre style="margin: 0;">-<span id="LC84" class="line" lang="diff"> import it.unimi.dsi.lang.MutableString;</span>
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<pre style="margin: 0;">-<span id="LC85" class="line" lang="diff"> import org.apache.commons.math.MathException;</span>
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="diff"><span class="p">@@ -371,15 +370,11 @@</span></span>
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<pre style="margin: 0;">-<span id="LC87" class="line" lang="diff"> assertEquals("fisher test equal expected result", 0.5044757698516504, results.getStatistic(info, fisher.statisticIds.get(0)), 0.001);</span>
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<pre style="margin: 0;">-<span id="LC88" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC89" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Fisher fisherTest = new Fisher();</span></span>
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<pre style="margin: 0;">-<span id="LC91" class="line" lang="diff"> final int totalCountInA = 1700;</span>
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<pre style="margin: 0;">-<span id="LC92" class="line" lang="diff"> final int totalCountInB = 170; // equal total in each group</span>
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<pre style="margin: 0;">-<span id="LC93" class="line" lang="diff"> final int sumCountInA = 90;</span>
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<pre style="margin: 0;">-<span id="LC94" class="line" lang="diff"> final int sumCountInB = 45; // half the counts in sample B</span>
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<pre style="margin: 0;">-<span id="LC95" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- fisherTest.fisher(totalCountInA, sumCountInA, totalCountInA + totalCountInB, sumCountInA + sumCountInB);</span></span>
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<pre style="margin: 0;">-<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<pre style="margin: 0;">-<span id="LC98" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final double pValue = fisherTest.getTwotail();</span></span>
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<pre style="margin: 0;">-<span id="LC99" class="line" lang="diff"> final double proportionTotalA = divide(totalCountInA, (totalCountInA + totalCountInB));</span>
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<pre style="margin: 0;">-<span id="LC100" class="line" lang="diff"> final double proportionTotalB = divide(totalCountInB, (totalCountInA + totalCountInB));</span>
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101
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<pre style="margin: 0;">-<span id="LC101" class="line" lang="diff"> final ChiSquareTest chisquare = new ChiSquareTestImpl();</span>
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102
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69
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/TestSamRecordParser.java</span></span>
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103
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70
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/TestSamRecordParser.java</span></span>
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104
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71
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"><span class="p">@@ -29,6 +29,7 @@</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">@@ -161,3 +128,286 @@ Last-Update: 2021-07-31</td>
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128
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<pre style="margin: 0;"> <span id="LC128" class="line" lang="diff"> @Test</span>
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129
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<pre style="margin: 0;"> <span id="LC129" class="line" lang="diff"> public void testUrlRange() throws IOException {</span>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="diff"> </span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/stats/TestStatistics.java</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/stats/TestStatistics.java</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="p">@@ -25,6 +25,7 @@</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> import org.apache.commons.math.MathException;</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> import org.apache.commons.math.stat.inference.ChiSquareTest;</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> import org.apache.commons.math.stat.inference.ChiSquareTestImpl;</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.Ignore;</span></span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> import org.junit.Test;</span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"> </span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"> import java.io.IOException;</span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="p">@@ -120,6 +121,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> results.write(new PrintWriter("test-results/out-stats.tsv"), '\t', deCalc);</span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> }</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> public void testTwoStats() {</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> final Random randomEngine = new Random(37);</span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestConcatSortedAlignmentReader.java</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestConcatSortedAlignmentReader.java</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="p">@@ -30,6 +30,7 @@</span></span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> </span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> import org.junit.Before;</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> import org.junit.BeforeClass;</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.Ignore;</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> import org.junit.Test;</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> </span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> import java.io.File;</span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="p">@@ -65,6 +66,7 @@</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> }</span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> </span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> </span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> @Test</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> public void testSortConcatWithGenomicRange() throws IOException {</span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"> final ConcatSortedAlignmentReader concat = new ConcatSortedAlignmentReader(basename1, basename2, basename3);</span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="p">@@ -102,6 +104,7 @@</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> }</span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> </span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> </span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> public void testSortConcatWithGenomicRangeSmaller() throws IOException {</span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> final ConcatSortedAlignmentReader concat = new ConcatSortedAlignmentReader(basename1, basename2, basename3);</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="p">@@ -120,6 +123,7 @@</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> }</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> </span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"> @Test</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> public void testSortConcatWithGenomicRangeSmaller2() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> final ConcatSortedAlignmentReader concat = new ConcatSortedAlignmentReader(basename1, basename2, basename3);</span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestRealignmentProcessor.java</span></span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/alignments/TestRealignmentProcessor.java</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="p">@@ -32,6 +32,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> import org.campagnelab.goby.modes.AbstractAlignmentToCompactMode;</span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> import org.campagnelab.goby.reads.RandomAccessSequenceInterface;</span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> import org.campagnelab.goby.reads.RandomAccessSequenceTestSupport;</span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.Ignore;</span></span>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> import org.junit.Test;</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> import java.io.IOException;</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="p">@@ -435,6 +436,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> }</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> }</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> </span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> public void testCase9() {</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> ObjectListIterator<Alignments.AlignmentEntry> iterator = new ObjectArrayList().iterator();</span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestDiscoverSequenceVariantsIndelGenotypes.java</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestDiscoverSequenceVariantsIndelGenotypes.java</span></span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="p">@@ -36,6 +36,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> import org.junit.AfterClass;</span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> import org.junit.Before;</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> import org.junit.BeforeClass;</span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.Ignore;</span></span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> import org.junit.Test;</span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> import java.io.*;</span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="p">@@ -77,6 +78,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"> mode.setTestGenome(genomeForTest);</span>
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"> public void testDiscoverWithIndelSamples() throws IOException, JSAPException {</span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestDiscoverSequenceVariantsMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestDiscoverSequenceVariantsMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="p">@@ -49,6 +49,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> import org.junit.AfterClass;</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> import org.junit.Before;</span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> import org.junit.BeforeClass;</span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.Ignore;</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"> import org.junit.Test;</span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> import java.io.*;</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="p">@@ -81,6 +82,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"> // assertNotNull("R engine must be available", GobyRengine.getInstance().getRengine());</span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> public void testDiscoverSomaticVariation() throws IOException, JSAPException {</span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="p">@@ -212,6 +214,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"> return dest;</span>
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"> public void testDiscoverAlleleImbalance() throws IOException, JSAPException {</span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="p">@@ -242,6 +245,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"> @Test</span>
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251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"> public void testDiscoverCheckSampleCountAssociation() throws IOException, JSAPException {</span>
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252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> </span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="p">@@ -552,6 +556,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"> </span>
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256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> </span>
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257
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> @Test</span>
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259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"> public void testGenotypes() throws IOException, JSAPException {</span>
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260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"> DiscoverSequenceVariantsMode mode = new DiscoverSequenceVariantsMode();</span>
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261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="p">@@ -572,6 +577,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"> }</span>
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264
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<pre style="margin: 0;">+<span id="LC264" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> @Test</span>
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267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> public void testQualityScoreAdjuster() {</span>
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268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"> QualityScoreFilter adjuster = new QualityScoreFilter();</span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="p">@@ -593,6 +599,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"> }</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"> </span>
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273
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"> public void testAdjustVarCount() {</span>
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"> QualityScoreFilter adjuster1 = new QualityScoreFilter();</span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="p">@@ -641,6 +648,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> public void testAdjustVarCount2() {</span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"> QualityScoreFilter adjuster1 = new QualityScoreFilter();</span>
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestLastToCompact.java</span></span>
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestLastToCompact.java</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="p">@@ -32,6 +32,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"> import static org.junit.Assert.assertTrue;</span>
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> import org.junit.Before;</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.Ignore;</span></span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> import org.junit.Test;</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> import java.io.File;</span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="p">@@ -39,6 +40,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> import java.io.IOException;</span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"> public class TestLastToCompact {</span>
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"> public void testLastToCompact1() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="p">@@ -154,6 +156,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> reader.close();</span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> public void testLastToCompact2() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="p">@@ -652,6 +655,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"> *</span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"> * @throws IOException</span>
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> public void testLastToCompactVariations() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestReformatCompactReadsMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestReformatCompactReadsMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="p">@@ -22,6 +22,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"> import org.campagnelab.goby.reads.ReadsReader;</span>
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"> import org.campagnelab.goby.reads.ReadsToTextWriter;</span>
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"> import org.apache.commons.io.FileUtils;</span>
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<pre style="margin: 0;">+<span id="LC325" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.Ignore;</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"> import org.junit.Test;</span>
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"> import java.io.File;</span>
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329
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="p">@@ -385,6 +386,7 @@</span></span>
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330
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> *</span>
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331
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> * @throws IOException if there is a problem reading or writing to the files</span>
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332
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"> */</span>
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333
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> public void reformatTransferMetaData() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"> final ReformatCompactReadsMode reformat = new ReformatCompactReadsMode();</span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestSortMode.java</span></span>
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338
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/modes/TestSortMode.java</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="p">@@ -24,6 +24,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"> import org.apache.commons.logging.LogFactory;</span>
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341
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"> import org.junit.AfterClass;</span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> import org.junit.BeforeClass;</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.Ignore;</span></span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> import org.junit.Test;</span>
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345
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> import java.io.File;</span>
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347
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"><span class="p">@@ -60,6 +61,7 @@</span></span>
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348
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> // FileUtils.forceDeleteOnExit(new File(BASE_TEST_DIR));</span>
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349
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"> }</span>
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350
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"> </span>
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351
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"> // check that large-sort can sort a small alignment (only one split):</span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"> public void sortSmall() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/modes/formats/TestCompareGroupsVCFOutputFormat.java</span></span>
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356
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/modes/formats/TestCompareGroupsVCFOutputFormat.java</span></span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="p">@@ -33,6 +33,7 @@</span></span>
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358
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"> import org.easymock.EasyMock;</span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"> import org.junit.Before;</span>
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"> import org.junit.BeforeClass;</span>
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.Ignore;</span></span>
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"> import org.junit.Test;</span>
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363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"> import java.io.PrintWriter;</span>
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="p">@@ -128,6 +129,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"> }</span>
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367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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370
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<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"> @Test</span>
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371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"> public void testNoDifference() throws Exception {</span>
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372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"> synchronized (GobyRengine.getInstance().getRengine()) {</span>
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373
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<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="p">@@ -154,6 +156,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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378
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<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"> @Test</span>
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379
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<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"> public void testAllelicDifference() throws Exception {</span>
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380
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<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"> synchronized (GobyRengine.getInstance().getRengine()) {</span>
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381
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<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/predictions/MergeIndelFromTest.java</span></span>
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382
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<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/predictions/MergeIndelFromTest.java</span></span>
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383
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<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="p">@@ -2,6 +2,7 @@</span></span>
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384
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<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"> </span>
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385
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<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"> import it.unimi.dsi.fastutil.objects.ObjectArraySet;</span>
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386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"> import org.campagnelab.goby.util.Variant;</span>
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387
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<pre style="margin: 0;">+<span id="LC387" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.junit.Ignore;</span></span>
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388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"> import org.junit.Test;</span>
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389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"> </span>
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390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"> import java.util.Set;</span>
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391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="p">@@ -59,6 +60,7 @@</span></span>
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392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"> */</span>
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393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"> </span>
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394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"> </span>
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395
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<pre style="margin: 0;">+<span id="LC395" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"> @Test</span>
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397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"> public void longestTailInDeletion() {</span>
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398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"> final Set<Variant.FromTo> fromTos = new ObjectArraySet<>(4);</span>
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399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="p">@@ -128,6 +130,7 @@</span></span>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"> */</span>
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401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"> </span>
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402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"> </span>
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403
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<pre style="margin: 0;">+<span id="LC403" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Ignore</span></span>
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404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"> @Test</span>
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405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"> public void longestTailInInsertion() {</span>
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406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"> final Set<Variant.FromTo> fromTos = new ObjectArraySet<>(4);</span>
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407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="p">@@ -183,4 +186,4 @@</span></span>
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408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"> assertNotNull(merge.mapped(originalAllele));</span>
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409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"> }</span>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"> }</span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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413
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<pre style="margin: 0;">+<span id="LC413" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/1f0226ab043686355a13f957d4060a95c7529140...48f2769114ecf743030944c266cd17ad8424f347#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</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">@@ -5,7 +5,7 @@ adapting_to_old_fastutil.patch</td>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">using_GeneratedMessageV3.patch</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">using_commons-cli.patch</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">using_correct_SamReader_api.patch</span>
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8
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="plaintext">computing_Fisher_test_pvalue.patch</span>
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9
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="plaintext">inclusions_in_SplitTranscriptsMode.patch</span>
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10
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9
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">catch_IOException_LineIterator.patch</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">computing_fisher_pvalue_hypergeom.patch</span>
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11
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11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">exclude_not_runnable_tests.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/1f0226ab043686355a13f957d4060a95c7529140...48f2769114ecf743030944c266cd17ad8424f347#f5606a935d95a2f20059a7ac1136f47b2edadbf6"><strong>debian/upstream/metadata</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Bug-Database: https://github.com/CampagneLaboratory/goby3/issues</span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Bug-Submit: https://github.com/CampagneLaboratory/goby3/issues/new</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">Repository: https://github.com/CampagneLaboratory/goby3.git</span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">Repository-Browse: https://github.com/CampagneLaboratory/goby3</span></pre>
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<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/1f0226ab043686355a13f957d4060a95c7529140...48f2769114ecf743030944c266cd17ad8424f347#68ef9f98c01c7eecd4c605cc26048a06f3304b79"><strong>debian/watch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">version=4</span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">opts="repacksuffix=+dfsg,dversionmangle=s/\+dfsg//g,repack,compression=xz" \</span>
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4
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> https://github.com/CampagneLaboratory/goby3/releases <span class="idiff left right">.*/archive/r*</span>@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/CampagneLaboratory/goby3/releases <span class="idiff left right">(?:.*?/)?r</span>@ANY_VERSION@@ARCHIVE_EXT@</span></pre>
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