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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/a4e593327f75bbb7e3148931fa1af9336c2c0ea8">a4e59332</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-10-19T17:32:32+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Using the Debian packaged implementation of bzip2
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/0e08c04cef6bd4f806966c12ed59063130e376c3">0e08c04c</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-10-19T17:33:15+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Changing old invocations of classes of fastutil
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/812a84eaa7465d0ed45971fa4178c3f28907144d">812a84ea</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-10-19T17:33:58+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Using GeneratedMessageV3 of protobuf instead of GeneratedMessage
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/acd6c100a16c35e66b7af536cd7a3f5c9d9602d8">acd6c100</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-10-19T17:35:17+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Adding dependencies to build goby-io
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/61862a5eb94f54576eba3d551384dc0fa9641cf9">61862a5e</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-11-10T17:55:19+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating dependencies and their management in d/maven.rules and d/maven.ignoreRules
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/65957a40dec3fd6b5ea8a24cb7b738c8ff97a7a2">65957a40</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-11-10T18:00:10+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Using classes of commons-cli instead of unpackaged ones
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/e3db8e8029bdba4eadfd29f4b9b4fc4e1b29aed4">e3db8e80</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-11-10T18:01:06+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Using the correct SamReader api
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/b8d5e1829b16aa7e51c92d016a1b8919b4e2be2d">b8d5e182</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-11-10T18:01:44+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Computing the Fisher p-value with a Debian-packaged tool
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/e2f3d3b9387e7433bbd83459a14c17aafe400f5c">e2f3d3b9</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-11-10T18:02:30+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Reading class GeneTranscriptRelationships from Goby archive
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/cfd4e5b3c3dc9e337522d78dce445ba03b1cdcc5">cfd4e5b3</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-11-10T18:03:05+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Catch the IOException launched by close() method of LineIterator
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/3a6ba7864cc9aaae4ae91907018455a1574af1f2">3a6ba786</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-11-10T18:03:59+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Modify a few tests when requiring unpackaged tools
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/295b3cbb37304c677ac3291bb1e5ffd04277f93d">295b3cbb</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-11-10T18:05:35+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Creating a symlink to test-data to perform the tests
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/libgoby-java/-/commit/1e72a3f187f726b1f77b1b27323c42aa69ca70cb">1e72a3f1</a></strong>
<div>
<span>by Pierre Gruet</span>
<i>at 2020-11-10T18:05:51+01:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Updating the TODO in d/changelog
</pre>
</li>
</ul>
<h4>16 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#26121dc92cd4cd9822d2e9e2b619b799bf9a51f4">
debian/maven.ignoreRules
</a>
</li>
<li class="file-stats">
<a href="#58530b38acb0fa3a65612c676abaea46c4a3f2f3">
debian/maven.rules
</a>
</li>
<li class="file-stats">
<a href="#729a4cacc53b031da47f89f5aee04741ec835694">
<span class="new-file">
+
debian/patches/adapting_to_old_fastutil.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8585405484f09930892f52fc8586f799991520f7">
debian/patches/adding_dependencies.patch
</a>
</li>
<li class="file-stats">
<a href="#feb3f16505e2aaa666cfa5d5bbefd0d3cde765d8">
<span class="new-file">
+
debian/patches/catch_IOException_LineIterator.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#7559433b4c62eba2f1020621fcb28c8c1c3e9ce5">
<span class="new-file">
+
debian/patches/computing_Fisher_test_pvalue.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#5befa0555f4aaaacd8314d84b172843245ca295f">
<span class="new-file">
+
debian/patches/exclude_not_runnable_tests.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#e5c767c2890f75ce61cf5fdf32589ce66eb14a98">
<span class="new-file">
+
debian/patches/inclusions_in_SplitTranscriptsMode.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#1f91261da06177ad9a3b396ac07d0c383bbf8b1a">
<span class="new-file">
+
debian/patches/using_GeneratedMessageV3.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#3c063e6429c2b2404cf4fc6ea6aaa059ff07e92c">
<span class="new-file">
+
debian/patches/using_commons-cli.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#ef745f5cc2f1850f044372eaa52b7f53ca4cc69f">
<span class="new-file">
+
debian/patches/using_correct_SamReader_api.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#cf3fc76fed161bccf82d0e694add0230b157ccc7">
<span class="new-file">
+
debian/patches/using_jbzip2.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
<hr>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="2" 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">@@ -2,14 +2,12 @@ libgoby-java (3.3.1+dfsg-1) UNRELEASED; urgency=medium</td>
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<td class="line_content" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext"></span>
</pre>
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<td class="diff-line-num new_line" data-linenumber="3" 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="LC3" class="line" lang="plaintext"> * Initial release (Closes: #<bug>)</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="4" 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="diff-line-num new_line" data-linenumber="4" 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="LC4" class="line" lang="plaintext"> TODO:</span>
</pre>
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<td class="diff-line-num new_line old" data-linenumber="5" 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="LC5" class="line" lang="plaintext"> - at least four packages are missing:</span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="6" 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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<td class="diff-line-num new_line old" data-linenumber="5" 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="LC6" class="line" lang="plaintext"> * edu.cornell.med.icb.identifier</span>
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<td class="diff-line-num old old_line" data-linenumber="7" 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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<td class="diff-line-num new_line old" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext"> * it.unimi.dsi.lang</span>
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<td class="diff-line-num old old_line" data-linenumber="8" 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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<td class="diff-line-num new_line old" data-linenumber="5" 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="LC8" class="line" lang="plaintext"> * it.unimi.dsi.logging</span>
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<td class="diff-line-num old old_line" data-linenumber="9" 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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<td class="diff-line-num new_line old" data-linenumber="5" 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="LC9" class="line" lang="plaintext"> * it.unimi.dsi.io</span>
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<td class="diff-line-num new old_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> - Packaging variationanalysis by Campagnelab, needed by goby.</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext"> - Go on investigating non-passing tests</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext"> (begun in debian/patches/exclude_not_runnable_tests.patch)</span>
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<td class="diff-line-num new_line" data-linenumber="8" 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="LC8" class="line" lang="plaintext"> - I have put some dependencies in debian/maven.ignoreRules but it may be</span>
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<td class="diff-line-num new_line" data-linenumber="9" 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="LC9" class="line" lang="plaintext"> wrong.</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> - See also https://lists.debian.org/debian-med/2013/02/msg00152.html,</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> although written for a previous upstream version of goby.</span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">-<span id="LC15" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> <span class="idiff left right">Mon, 24 Aug 2020 11:48:00 +02</span>00</span></pre>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> -- Pierre Gruet <pgtdebian@free.fr> <span class="idiff left right">Tue, 10 Nov 2020 17:50:48 +01</span>00</span></pre>
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<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</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">@@ -17,6 +17,7 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> libcommons-lang-java,</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> libcommons-logging-java,</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> libcommons-math-java,</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> libcommons-cli-java,</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> liblog4j1.2-java,</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> libexec-maven-plugin-java,</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"> libmaven-assembly-plugin-java,</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -29,7 +30,19 @@ Build-Depends: debhelper-compat (= 13),</td>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext"> libhtsjdk-java,</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext"> libfastutil-java,</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext"> protobuf-compiler,</span>
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<pre style="margin: 0;">-<span id="LC32" class="line" lang="plaintext"> libjsap-java</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext"> libjsap-java,</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext"> libdsiutils-java,</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> libicb-utils-java,</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> libreflections-java,</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> libpj-java,</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext"> libprotobuf-dev,</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> libpcre3-dev,</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> pkg-config,</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> r-cran-rjava,</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext"> libeasymock-java <!nocheck>,</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext"> junit4 <!nocheck>,</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> testng <!nocheck>,</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> libpicard-java <!nocheck></span>
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33
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46
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<pre style="margin: 0;"> <span id="LC46" class="line" lang="plaintext">Standards-Version: 4.5.0</span>
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34
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47
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="plaintext">Vcs-Browser: https://anonscm.debian.org/cgit/debian-med/libgoby-java.git</span>
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35
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<td class="diff-line-num new_line" data-linenumber="48" 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">
48
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="plaintext">Vcs-Git: https://anonscm.debian.org/git/debian-med/libgoby-java.git</span>
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<li id="26121dc92cd4cd9822d2e9e2b619b799bf9a51f4">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#26121dc92cd4cd9822d2e9e2b619b799bf9a51f4"><strong>debian/maven.ignoreRules</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">@@ -3,7 +3,9 @@ org.sonatype.plugins nexus-staging-maven-plugin * * * *</td>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">kr.motd.maven os-maven-plugin * * * *</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">pl.project13.maven git-commit-id-plugin * * * *</span>
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<td class="diff-line-num new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext">org.apache.maven.plugins maven-verifier-plugin * * * *</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext">org.campagnelab.icb icb-utils * * * *</span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="plaintext">it.unimi.dsi dsiutils * * * *</span>
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<td class="diff-line-num new_line old" data-linenumber="6" 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="LC8" class="line" lang="plaintext">org.reflections reflections * * * *</span>
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9
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<td class="diff-line-num 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">
6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">com.github.lucarosellini.rJava JRI * * * *</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">org.deeplearning4j * * * * *</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">edu.mssm.crover cli * * * *</span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">edu.cornell.med.icb tisim-api * * * *</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">org.nd4j * * * * *</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">junit-addons junit-addons * * * *</span></pre>
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<li id="58530b38acb0fa3a65612c676abaea46c4a3f2f3">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#58530b38acb0fa3a65612c676abaea46c4a3f2f3"><strong>debian/maven.rules</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" 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="5" 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">@@ -5,3 +5,10 @@ org.apache.maven.plugins maven-antrun-plugin jar s/.*/1.8/ * *</td>
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5
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<td class="diff-line-num new_line" data-linenumber="5" 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="LC5" class="line" lang="plaintext">org.codehaus.mojo build-helper-maven-plugin jar s/.*/3.0.0/ * *</span>
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<td class="diff-line-num 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">
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<td class="diff-line-num 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">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">org.apache.maven.plugins maven-dependency-plugin jar s/.*/3.1.1/ * *</span>
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">org.apache.maven.plugins maven-javadoc-plugin jar s/.*/3.0.1/ * *</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">it.unimi.dsi dsiutils jar s/.*/debian/ * *</span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">org.campagnelab.icb icb-utils jar s/.*/debian/ * *</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">org.reflections reflections jar s/.*/debian/ * *</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">s/org.campagnelab.ext/com.martiansoftware/ jsap jar s/.*/debian/ * *</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">junit junit jar s/.*/4.x/ * *</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">org.easymock easymock jar s/.*/debian/ * *</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext">com.github.samtools htsjdk jar s/.*/debian/ * *</span></pre>
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<li id="729a4cacc53b031da47f89f5aee04741ec835694">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#729a4cacc53b031da47f89f5aee04741ec835694"><strong>debian/patches/adapting_to_old_fastutil.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.java</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/alignments/ConcatSortedAlignmentReader.java</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> package org.campagnelab.goby.alignments;</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import it.unimi.dsi.fastutil.AbstractPriorityQueue;</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import it.unimi.dsi.fastutil.PriorityQueue;</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> import it.unimi.dsi.fastutil.objects.ObjectArrayPriorityQueue;</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> import it.unimi.dsi.fastutil.objects.ObjectHeapPriorityQueue;</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import org.apache.commons.logging.Log;</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">@@ -40,7 +40,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> public class ConcatSortedAlignmentReader extends ConcatAlignmentReader {</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 class="gd" style="color: #000; background-color: #fdd;">- AbstractPriorityQueue<Bucket> entryHeap;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PriorityQueue<Bucket> entryHeap;</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> private static AlignmentPositionComparator comparator = new AlignmentPositionComparator();</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> private boolean[] nextLoadedForReader;</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> private Bucket[] buckets;</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/alignments/processors/LocalSortProcessor.java</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/alignments/processors/LocalSortProcessor.java</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -21,7 +21,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> import edu.cornell.med.icb.identifier.IndexedIdentifier;</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> import org.campagnelab.goby.alignments.Alignments;</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> import org.campagnelab.goby.reads.RandomAccessSequenceInterface;</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import it.unimi.dsi.fastutil.AbstractPriorityQueue;</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;">+import it.unimi.dsi.fastutil.PriorityQueue;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> import it.unimi.dsi.fastutil.objects.ObjectHeapPriorityQueue;</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> import java.io.IOException;</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="p">@@ -38,7 +38,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> * Time: 10:49 AM</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> public class LocalSortProcessor implements AlignmentProcessorInterface {</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;">- AbstractPriorityQueue<Alignments.AlignmentEntry> entryHeap;</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;">+ PriorityQueue<Alignments.AlignmentEntry> entryHeap;</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> AlignmentProcessorInterface delegate;</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> * We store at most alignments for 30 consecutive genomic positions. 30 is chosen because it is much larger than</span></pre>
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<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#8585405484f09930892f52fc8586f799991520f7"><strong>debian/patches/adding_dependencies.patch</strong></a>
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1
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="diff"><span class="p">Description: Adding missing dependencies to goby-io/pom.xml</span></span>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">-<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2020-<span class="idiff left right">08-24</span></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Last-Update: 2020-<span class="idiff left right">10-31</span></span></span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff">--- a/goby-io/pom.xml</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-io/pom.xml</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="29" 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="29" 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">@@ -29,3 +29,59 @@ Last-Update: 2020-08-24</td>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"> </dependencies></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> </project></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/pom.xml</span></span>
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<pre style="margin: 0;">+<span id="LC33" 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="LC34" class="line" lang="diff"><span class="p">@@ -140,6 +140,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> <version>2.6</version></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </dependency></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> <dependency></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;">+ <groupId>commons-cli</groupId></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;">+ <artifactId>commons-cli</artifactId></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;">+ <version>debian</version></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;">+ </dependency></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;">+ <dependency></span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> <groupId>commons-logging</groupId></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> <artifactId>commons-logging</artifactId></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> <version>1.1.1</version></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="p">@@ -193,7 +198,9 @@</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> <dependency></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> <groupId>org.rosuda.REngine</groupId></span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> <artifactId>REngine</artifactId></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- <version>2.1.0</version></span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" 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="LC52" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <scope>system</scope></span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <systemPath>/usr/lib/R/site-library/rJava/jri/JRI.jar</systemPath></span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </dependency></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> <dependency></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> <groupId>com.github.lucarosellini.rJava</groupId></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="p">@@ -240,9 +247,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> <dependency></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> <groupId>edu.rit.pj</groupId></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> <artifactId>pj</artifactId></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;">- <version>1.0</version></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;">- <scope>system</scope></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;">- <systemPath>${basedir}/../lib/pj20091226.jar</systemPath></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;">+ <version>debian</version></span></span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> </dependency></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> <dependency></span>
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> <groupId>edu.mssm.crover</groupId></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="p">@@ -339,10 +344,18 @@</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> </dependency></span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> <dependency></span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <groupId>org.testng</groupId></span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <artifactId>testng</artifactId></span></span>
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<pre style="margin: 0;">+<span id="LC74" 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="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <scope>test</scope></span></span>
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<pre style="margin: 0;">+<span id="LC76" 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="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <dependency></span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> <groupId>com.github.broadinstitute</groupId></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> <artifactId>picard</artifactId></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> <version>2.6.0</version></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;">- <scope>test</scope></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;">+ <scope>system</scope></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;">+ <systemPath>/usr/share/java/picard.jar</systemPath></span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> </dependency></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> <dependency></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> <groupId>it.unimi.dsi</groupId></span></pre>
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<li id="feb3f16505e2aaa666cfa5d5bbefd0d3cde765d8">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#feb3f16505e2aaa666cfa5d5bbefd0d3cde765d8"><strong>debian/patches/catch_IOException_LineIterator.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: Catch the IOException launched by close() method of LineIterator</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Last-Update: 2020-11-03</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/EmpiricalPMode.java</span>
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7
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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/modes/EmpiricalPMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -342,7 +342,12 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> Object next = it.next();</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> lineCount++;</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> }</span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- it.close();</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try {</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ it.close();</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } catch (IOException e) {</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.err.println("Could not close LineIterator on " + inputFilename);</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.exit(1);</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> return lineCount;</span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> }</span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> </span></pre>
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<li id="7559433b4c62eba2f1020621fcb28c8c1c3e9ce5">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#7559433b4c62eba2f1020621fcb28c8c1c3e9ce5"><strong>debian/patches/computing_Fisher_test_pvalue.patch</strong></a>
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1
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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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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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3
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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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4
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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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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"></span>
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6
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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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7
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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/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#5befa0555f4aaaacd8314d84b172843245ca295f"><strong>debian/patches/exclude_not_runnable_tests.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: modify a few tests when requiring unpackaged tools</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> junitx.framework is not packaged, the test files TestSplicedSamHelper.java and</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> TestAlignmentReader.java, that use it, are deactivated in</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> goby-distribution/pom.xml.</span>
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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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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="p">Last-Update: 2020-11-08</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff">--- a/goby-distribution/pom.xml</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;">+++ b/goby-distribution/pom.xml</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="p">@@ -39,6 +39,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> <configuration></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> <source>${java.version}</source></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> <target>${java.version}</target></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <testExcludes></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;">+ <exclude>**/TestSplicedSamHelper.java</exclude></span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <exclude>**/TestAlignmentReader.java</exclude></span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </testExcludes></span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </configuration></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </plugin></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> <plugin></span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="p">@@ -73,6 +77,16 @@</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </executions></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> </plugin></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> <plugin></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;">+ <groupId>org.apache.maven.plugins</groupId></span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <artifactId>maven-surefire-plugin</artifactId></span></span>
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<pre style="margin: 0;">+<span id="LC32" 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="LC33" 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="LC34" 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="LC35" 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="LC36" 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="LC37" 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="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ </plugin></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;">+ <plugin></span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> <artifactId>maven-assembly-plugin</artifactId></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> <version>2.6</version></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> <configuration></span>
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<pre style="margin: 0;">+<span id="LC43" 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="LC44" 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="LC45" class="line" lang="diff"><span class="p">@@ -18,7 +18,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> package org.campagnelab.goby.R;</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC49" 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="LC50" class="line" lang="diff"> import org.apache.commons.lang.ArrayUtils;</span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> import org.junit.AfterClass;</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> import static org.junit.Assert.assertEquals;</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="p">@@ -151,18 +150,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> result.getAlternativeHypothesis());</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> }</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 class="gd" style="color: #000; background-color: #fdd;">- /**</span></span>
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<pre style="margin: 0;">+<span id="LC58" 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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59
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<pre style="margin: 0;">+<span id="LC59" 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="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- */</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" 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="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void twoTailed() {</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" 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="LC64" 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="LC65" 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="LC66" 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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67
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<pre style="margin: 0;">+<span id="LC67" 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="LC68" 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="LC69" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> /**</span>
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<pre style="margin: 0;">+<span id="LC71" 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="LC72" 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="LC73" 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="LC74" class="line" lang="diff"><span class="p">@@ -19,7 +19,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> package org.campagnelab.goby.stats;</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"> import org.campagnelab.goby.R.FisherExact;</span>
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<pre style="margin: 0;">+<span id="LC78" 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="LC79" class="line" lang="diff"> import it.unimi.dsi.fastutil.objects.ObjectArrayList;</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> import it.unimi.dsi.lang.MutableString;</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> import org.apache.commons.math.MathException;</span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="p">@@ -371,15 +370,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC83" 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="LC84" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC86" 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="LC87" class="line" lang="diff"> final int totalCountInA = 1700;</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> final int totalCountInB = 170; // equal total in each group</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> final int sumCountInA = 90;</span>
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<pre style="margin: 0;">+<span id="LC90" 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="LC91" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC92" 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="LC93" 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="LC94" 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="LC95" class="line" lang="diff"> final double proportionTotalA = divide(totalCountInA, (totalCountInA + totalCountInB));</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> final double proportionTotalB = divide(totalCountInB, (totalCountInA + totalCountInB));</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> final ChiSquareTest chisquare = new ChiSquareTestImpl();</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;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/TestSamRecordParser.java</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;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/TestSamRecordParser.java</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="p">@@ -29,6 +29,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> import org.apache.commons.io.FilenameUtils;</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> import org.slf4j.Logger;</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> import org.junit.BeforeClass;</span>
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<pre style="margin: 0;">+<span id="LC104" 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="LC105" class="line" lang="diff"> import org.junit.Test;</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> import org.slf4j.LoggerFactory;</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"><span class="p">@@ -425,6 +426,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> *</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> * @throws IOException error</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC112" 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="LC113" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> public void testRoundTripTrickySpliced18() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> final RoundTripAlignment rtc = new RoundTripAlignment();</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="p">@@ -672,6 +674,7 @@</span></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"> * @throws java.io.IOException error</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC120" 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="LC121" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> public void testTestTargetIndexCreation() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> final RoundTripAlignment rtc = new RoundTripAlignment();</span></pre>
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<br>
</li>
<li id="e5c767c2890f75ce61cf5fdf32589ce66eb14a98">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#e5c767c2890f75ce61cf5fdf32589ce66eb14a98"><strong>debian/patches/inclusions_in_SplitTranscriptsMode.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: reading class GeneTranscriptRelationships from Goby archive</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"> The above-named class is in the archive of Goby and thus does not need to be read elsewhere.</span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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4
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2020-11-02</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SplitTranscriptsMode.java</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SplitTranscriptsMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -24,7 +24,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> import org.campagnelab.goby.readers.FastXEntry;</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import org.campagnelab.goby.readers.FastXReader;</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> import edu.cornell.med.icb.identifier.IndexedIdentifier;</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import edu.cornell.med.icb.tissueinfo.similarity.GeneTranscriptRelationships;</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;">+import org.campagnelab.goby.alignments.filters.GeneTranscriptRelationships;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> import it.unimi.dsi.fastutil.ints.Int2IntMap;</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> import it.unimi.dsi.fastutil.ints.Int2IntOpenHashMap;</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> import it.unimi.dsi.fastutil.ints.Int2ObjectMap;</span></pre>
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<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<pre style="margin: 0;"> <span id="LC1" class="line" lang="plaintext">protoc.patch</span>
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">adding_dependencies.patch</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext">using_jbzip2.patch</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext">adapting_to_old_fastutil.patch</span>
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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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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">using_commons-cli.patch</span>
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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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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext">inclusions_in_SplitTranscriptsMode.patch</span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext">catch_IOException_LineIterator.patch</span>
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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/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#1f91261da06177ad9a3b396ac07d0c383bbf8b1a"><strong>debian/patches/using_GeneratedMessageV3.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentCollectionHandler.java</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/alignments/AlignmentCollectionHandler.java</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> import com.google.protobuf.ByteString;</span>
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<td class="diff-line-num new new_line" data-linenumber="6" 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="LC6" class="line" lang="diff"> import com.google.protobuf.CodedInputStream;</span>
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<td class="diff-line-num new new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import com.google.protobuf.GeneratedMessage;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import com.google.protobuf.GeneratedMessageV3;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> import com.google.protobuf.Message;</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> import org.campagnelab.goby.compression.*;</span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import org.campagnelab.goby.compression.FastArithmeticCoder;</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="p">@@ -177,7 +177,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> @Override</span>
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<td class="diff-line-num new new_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public GeneratedMessage parse(final InputStream uncompressedStream) throws IOException {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="17" 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="LC17" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public GeneratedMessageV3 parse(final InputStream uncompressedStream) throws IOException {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="18" 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="LC18" class="line" lang="diff"> final byte[] bytes = IOUtils.toByteArray(uncompressedStream);</span>
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<td class="diff-line-num new new_line" data-linenumber="19" 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="LC19" class="line" lang="diff"> final CodedInputStream codedInput = CodedInputStream.newInstance(bytes);</span>
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<td class="diff-line-num new new_line" data-linenumber="20" 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="LC20" class="line" lang="diff"> codedInput.setSizeLimit(Integer.MAX_VALUE);</span>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.java</span></span>
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<td class="diff-line-num new new_line" 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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/compression/FastBufferedMessageChunksReader.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="23" 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="LC23" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="24" 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="LC24" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="25" 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="LC25" class="line" lang="diff"> package org.campagnelab.goby.compression;</span>
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<td class="diff-line-num new new_line" 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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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import com.google.protobuf.GeneratedMessage;</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;">+import com.google.protobuf.GeneratedMessageV3;</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> import org.campagnelab.goby.exception.GobyRuntimeException;</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> import it.unimi.dsi.fastutil.bytes.ByteSet;</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> import it.unimi.dsi.fastutil.io.FastBufferedInputStream;</span>
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<td class="diff-line-num new new_line" data-linenumber="32" 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="LC32" class="line" lang="diff"><span class="p">@@ -215,7 +215,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="33" 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="LC33" class="line" lang="diff"> * @return True if the input has more entries, False otherwise.</span>
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<td class="diff-line-num new new_line" data-linenumber="34" 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="LC34" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> @Override</span>
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<td class="diff-line-num new new_line" data-linenumber="36" 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="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public boolean hasNext(final GeneratedMessage collection, final int collectionSize) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="37" 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="LC37" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public boolean hasNext(final GeneratedMessageV3 collection, final int collectionSize) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="38" 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="LC38" class="line" lang="diff"> if (collection == null || entryIndex >= collectionSize) {</span>
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<td class="diff-line-num new new_line" data-linenumber="39" 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="LC39" class="line" lang="diff"> if (input != null) {</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> try {</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksReader.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="42" 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="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksReader.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="43" 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="LC43" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> package org.campagnelab.goby.compression;</span>
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<td class="diff-line-num new new_line" data-linenumber="46" 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="LC46" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="47" 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="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import com.google.protobuf.GeneratedMessage;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="48" 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="LC48" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import com.google.protobuf.GeneratedMessageV3;</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> import org.campagnelab.goby.exception.GobyRuntimeException;</span>
</pre>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> import org.apache.commons.io.IOUtils;</span>
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<td class="diff-line-num new new_line" data-linenumber="51" 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="LC51" class="line" lang="diff"> import org.apache.commons.logging.Log;</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="p">@@ -85,7 +85,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> * @param collectionSize The size of the current collection (can be zero).</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> * @return True if the input has more entries, False otherwise.</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public boolean hasNext(final GeneratedMessage collection, final int collectionSize) {</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public boolean hasNext(final GeneratedMessageV3 collection, final int collectionSize) {</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> if (collection == null || entryIndex >= collectionSize) {</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"> if (in == null) {</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> compressedBytes = null;</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;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksWriter.java</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;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/compression/MessageChunksWriter.java</span></span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="p">@@ -124,7 +124,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> * @param collectionBuilder The builder prepared with the growing collection of entries.</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> * @throws IOException if there was an error writing the entries</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> */</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;">- public void writeAsNeeded(final com.google.protobuf.GeneratedMessage.Builder collectionBuilder) {</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void writeAsNeeded(final com.google.protobuf.GeneratedMessageV3.Builder collectionBuilder) {</span></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"> writeAsNeeded(collectionBuilder, 1);</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="p">@@ -139,7 +139,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> * was just appended.</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> * @throws IOException if there was an error writing the entries</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> */</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;">- public synchronized long writeAsNeeded(final com.google.protobuf.GeneratedMessage.Builder collectionBuilder,</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;">+ public synchronized long writeAsNeeded(final com.google.protobuf.GeneratedMessageV3.Builder collectionBuilder,</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> final int multiplicity) {</span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> totalEntriesWritten += Math.max(1, multiplicity);</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> if (++numAppended >= numEntriesPerChunk) {</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="p">@@ -162,7 +162,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> *</span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> * @param collectionBuilder The builder prepared with the growing collection of entries.</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> */</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public synchronized void flush(final com.google.protobuf.GeneratedMessage.Builder collectionBuilder) {</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;">+ public synchronized void flush(final com.google.protobuf.GeneratedMessageV3.Builder collectionBuilder) {</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> // Write the separation between two chunks: eight bytes with value 0xFF.</span>
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88
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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"> // If we are flushing a completely empty file, that's OK, the flush() should occur.</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="p">@@ -221,7 +221,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> * @param collectionBuilder The builder prepared with the growing collection of entries.</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> * @throws IOException if there is a problem closing the stream unerlying stream</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> */</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void close(final com.google.protobuf.GeneratedMessage.Builder collectionBuilder)</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void close(final com.google.protobuf.GeneratedMessageV3.Builder collectionBuilder)</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> flush(collectionBuilder);</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> out.writeByte(0xFF); // termination codec is always GZIP</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/compression/ProtobuffCollectionHandler.java</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/compression/ProtobuffCollectionHandler.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="p">@@ -18,7 +18,7 @@</span></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"> package org.campagnelab.goby.compression;</span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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="LC104" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import com.google.protobuf.GeneratedMessage;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import com.google.protobuf.GeneratedMessageV3;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="107" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> import com.google.protobuf.Message;</span>
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<td class="diff-line-num new new_line" data-linenumber="108" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="109" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> import java.io.ByteArrayOutputStream;</span>
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<td class="diff-line-num new new_line" data-linenumber="110" 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="LC110" class="line" lang="diff"><span class="p">@@ -46,7 +46,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="111" 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="LC111" class="line" lang="diff"> */</span>
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<td class="diff-line-num new new_line" data-linenumber="112" 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="LC112" class="line" lang="diff"> public int getType();</span>
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<td class="diff-line-num new new_line" data-linenumber="113" 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="LC113" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="114" 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="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public GeneratedMessage parse(InputStream uncompressedStream) throws IOException;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public GeneratedMessageV3 parse(InputStream uncompressedStream) throws IOException;</span></span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="117" 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="LC117" class="line" lang="diff"> /**</span>
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<td class="diff-line-num new new_line" data-linenumber="118" 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="LC118" class="line" lang="diff"> * Transform a collection to a stream of compressed bits, and return the left-over collection.</span>
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<td class="diff-line-num new new_line" data-linenumber="119" 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="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/compression/SequenceBaseInfoCollectionHandler.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="120" 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="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/compression/SequenceBaseInfoCollectionHandler.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="121" 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="LC121" class="line" lang="diff"><span class="p">@@ -1,7 +1,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="122" 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="LC122" class="line" lang="diff"> package org.campagnelab.goby.compression;</span>
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<td class="diff-line-num new new_line" data-linenumber="123" 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="LC123" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="124" 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="LC124" class="line" lang="diff"> import com.google.protobuf.CodedInputStream;</span>
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<td class="diff-line-num new new_line" data-linenumber="125" 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="LC125" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import com.google.protobuf.GeneratedMessage;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="126" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import com.google.protobuf.GeneratedMessageV3;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="127" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> import com.google.protobuf.Message;</span>
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<td class="diff-line-num new new_line" data-linenumber="128" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> import org.apache.commons.io.IOUtils;</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="p">@@ -21,7 +21,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> @Override</span>
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<td class="diff-line-num new new_line" data-linenumber="134" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public GeneratedMessage parse(final InputStream compressedBytes) throws IOException {</span></span>
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<td class="diff-line-num new new_line" 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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public GeneratedMessageV3 parse(final InputStream compressedBytes) throws IOException {</span></span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> final byte[] bytes = IOUtils.toByteArray(compressedBytes);</span>
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<td class="diff-line-num new new_line" data-linenumber="137" 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="LC137" class="line" lang="diff"> final CodedInputStream codedInput = CodedInputStream.newInstance(bytes);</span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> codedInput.setSizeLimit(Integer.MAX_VALUE);</span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/compression/SequenceSegmentInfoCollectionHandler.java</span></span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/compression/SequenceSegmentInfoCollectionHandler.java</span></span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"><span class="p">@@ -1,7 +1,7 @@</span></span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> package org.campagnelab.goby.compression;</span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> import com.google.protobuf.CodedInputStream;</span>
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<td class="diff-line-num new new_line" 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="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import com.google.protobuf.GeneratedMessage;</span></span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import com.google.protobuf.GeneratedMessageV3;</span></span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> import com.google.protobuf.Message;</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="148" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"> import org.apache.commons.io.IOUtils;</span>
</pre>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> import org.campagnelab.dl.varanalysis.protobuf.BaseInformationRecords;</span>
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<td class="diff-line-num new new_line" data-linenumber="150" 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="LC150" class="line" lang="diff"><span class="p">@@ -27,7 +27,7 @@</span></span>
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<td class="diff-line-num new new_line" data-linenumber="151" 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="LC151" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"> @Override</span>
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<td class="diff-line-num new new_line" data-linenumber="154" 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">
154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public GeneratedMessage parse(InputStream uncompressedStream) throws IOException {</span></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;">+ public GeneratedMessageV3 parse(InputStream uncompressedStream) throws IOException {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="156" 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="LC156" class="line" lang="diff"> final byte[] bytes = IOUtils.toByteArray(uncompressedStream);</span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> final CodedInputStream codedInput = CodedInputStream.newInstance(bytes);</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> codedInput.setSizeLimit(Integer.MAX_VALUE);</span>
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<td class="diff-line-num new new_line" data-linenumber="159" 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="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadProtobuffCollectionHandler.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="160" 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="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/reads/ReadProtobuffCollectionHandler.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="161" 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="LC161" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> package org.campagnelab.goby.reads;</span>
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<td class="diff-line-num new new_line" data-linenumber="163" 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="LC163" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="164" 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="LC164" class="line" lang="diff"> import com.google.protobuf.CodedInputStream;</span>
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<td class="diff-line-num new new_line" data-linenumber="165" 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="LC165" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import com.google.protobuf.GeneratedMessage;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="166" 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="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import com.google.protobuf.GeneratedMessageV3;</span></span>
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"> import com.google.protobuf.Message;</span>
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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> import org.campagnelab.goby.compression.ProtobuffCollectionHandler;</span>
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<td class="diff-line-num new new_line" 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="diff"> import org.apache.commons.io.IOUtils;</span>
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<td class="diff-line-num new new_line" 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">
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"><span class="p">@@ -42,7 +42,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> @Override</span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public GeneratedMessage parse(final InputStream compressedBytes) throws IOException {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public GeneratedMessageV3 parse(final InputStream compressedBytes) throws IOException {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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="LC176" class="line" lang="diff"> final byte[] bytes = IOUtils.toByteArray(compressedBytes);</span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> final CodedInputStream codedInput = CodedInputStream.newInstance(bytes);</span>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> codedInput.setSizeLimit(Integer.MAX_VALUE);</span></pre>
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<li id="3c063e6429c2b2404cf4fc6ea6aaa059ff07e92c">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#3c063e6429c2b2404cf4fc6ea6aaa059ff07e92c"><strong>debian/patches/using_commons-cli.patch</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: using classes of commons-cli instead of unpackaged ones</span></span>
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2
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></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: 2020-11-02</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/algorithmic/algorithm/dmr/EstimatedDistribution.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/algorithmic/algorithm/dmr/EstimatedDistribution.java</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> package org.campagnelab.goby.algorithmic.algorithm.dmr;</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import org.campagnelab.goby.algorithmic.algorithm.FenwickTree;</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 edu.mssm.crover.cli.CLI;</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;">+import org.apache.commons.cli.*;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> import it.unimi.dsi.fastutil.ints.IntArrayList;</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> import it.unimi.dsi.fastutil.io.BinIO;</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> import it.unimi.dsi.fastutil.objects.ObjectArrayList;</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="p">@@ -240,68 +240,113 @@</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> public static void main(final String[] args) throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- boolean printDensity = CLI.isKeywordGiven(args, "--print-density");</span></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;">- boolean printObservations = CLI.isKeywordGiven(args, "--print-observations");</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;">- String filename = CLI.getOption(args, "-f", null);</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String outputFilename = CLI.getOption(args, "-o", "out.tsv");</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PrintWriter outWriter = new PrintWriter(new FileWriter(outputFilename));</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (printDensity) {</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EstimatedDistribution estimated = null;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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29
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- try {</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- estimated = load(filename);</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String statName = estimated.getStatAdaptor().statName();</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println("Statistic=" + statName);</span></span>
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33
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println("binning strategy=" + estimated.getBinningStrategy().getName());</span></span>
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34
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int index = 0;</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;">- outWriter.println("midPointSumTotal\tsumTotal range\t" + statName + "\tcount-at-" + statName);</span></span>
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36
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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 BinningStrategy binningStrategy = estimated.getBinningStrategy();</span></span>
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37
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (final FenwickTree tree : estimated.densitities) {</span></span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (tree != null) {</span></span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int low = binningStrategy.getLowerBound(index);</span></span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int high = binningStrategy.getUpperBound(index);</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int midPointSumTotal = binningStrategy.getMidpoint(index);</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.printf("low=%d high=%d midPoint=%d %n", low, high, midPointSumTotal);</span></span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final long maxCumulative = tree.getCumulativeCount(tree.size() - 2);</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (int scaledStatistic = 0; scaledStatistic < tree.size() - 1; scaledStatistic++) {</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final long cumulativeCountAt = tree.getCumulativeCount(scaledStatistic);</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final long cumulativeCountAfter = tree.getCumulativeCount(scaledStatistic + 1);</span></span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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<td class="diff-line-num new new_line" data-linenumber="49" 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">
49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outWriter.printf("%d\t[%d-%d]\t%g\t%d%n", midPointSumTotal, binningStrategy.getLowerBound(index),</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- binningStrategy.getUpperBound(index), estimated.unscale(scaledStatistic), cumulativeCountAfter - cumulativeCountAt);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="51" 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">
51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (cumulativeCountAfter == maxCumulative) {</span></span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- break;</span></span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Options options = new Options();</span></span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option pDensity = new Option("printDensity", "print-density", false, "print density");</span></span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pDensity.setRequired(false);</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(pDensity);</span></span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option pObservations = new Option("printObservations", "print-observations", false, "print observations");</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pObservations.setRequired(false);</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(pObservations);</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option fname = new Option("filename", "filename", true, "filename");</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fname.setRequired(false);</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(fname);</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option o = new Option("o", "o", true, "output filename");</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ o.setRequired(false);</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(o);</span></span>
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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;">+</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommandLineParser parser = new DefaultParser();</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommandLine cmd;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="73" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String filename;</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String outputFilename;</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ boolean printDensity;</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ boolean printObservations;</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="79" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd = parser.parse(options, args);</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ printDensity = cmd.hasOption("printDensity");</span></span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ printObservations = cmd.hasOption("printObservations");</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("f")) {</span></span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ filename = cmd.getOptionValue("f");</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;">+ }</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ filename = null;</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("o")) {</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outputFilename = cmd.getOptionValue("o");</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outputFilename = new String("out.tsv");</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="97" 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">
97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="98" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PrintWriter outWriter = new PrintWriter(new FileWriter(outputFilename));</span></span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (printDensity) {</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EstimatedDistribution estimated = null;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="101" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="102" 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">
102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="103" 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">
103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ estimated = load(filename);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="104" 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">
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;">+ String statName = estimated.getStatAdaptor().statName();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="105" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.out.println("Statistic=" + statName);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="106" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.out.println("binning strategy=" + estimated.getBinningStrategy().getName());</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int index = 0;</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outWriter.println("midPointSumTotal\tsumTotal range\t" + statName + "\tcount-at-" + statName);</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final BinningStrategy binningStrategy = estimated.getBinningStrategy();</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (final FenwickTree tree : estimated.densitities) {</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (tree != null) {</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int low = binningStrategy.getLowerBound(index);</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int high = binningStrategy.getUpperBound(index);</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="115" 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">
115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int midPointSumTotal = binningStrategy.getMidpoint(index);</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.out.printf("low=%d high=%d midPoint=%d %n", low, high, midPointSumTotal);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="117" 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">
117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final long maxCumulative = tree.getCumulativeCount(tree.size() - 2);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="118" 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">
118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (int scaledStatistic = 0; scaledStatistic < tree.size() - 1; scaledStatistic++) {</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final long cumulativeCountAt = tree.getCumulativeCount(scaledStatistic);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="120" 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">
120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final long cumulativeCountAfter = tree.getCumulativeCount(scaledStatistic + 1);</span></span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="122" 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">
122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outWriter.printf("%d\t[%d-%d]\t%g\t%d%n", midPointSumTotal, binningStrategy.getLowerBound(index),</span></span>
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<td class="diff-line-num new new_line" data-linenumber="123" 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">
123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ binningStrategy.getUpperBound(index), estimated.unscale(scaledStatistic), cumulativeCountAfter - cumulativeCountAt);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="124" 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">
124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cumulativeCountAfter == maxCumulative) {</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;">+ break;</span></span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> }</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> }</span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- index++;</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ index++;</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> </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;">+ }</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;">+ outWriter.close();</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;">+ } catch (Exception e) {</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;">+ e.printStackTrace();</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;">+ System.exit(1);</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;">- outWriter.close();</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;">- } catch (Exception e) {</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;">- e.printStackTrace();</span></span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.exit(1);</span></span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></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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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (printObservations) {</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (printObservations) {</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> </span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EstimatedDistribution estimated = null;</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EstimatedDistribution estimated = null;</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"><span class="gd" style="color: #000; background-color: #fdd;">- try {</span></span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- estimated = load(filename);</span></span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String statName = estimated.getStatAdaptor().statName();</span></span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outWriter.println("tscaled-" + statName + "\t" + statName + "\tcovariates\n");</span></span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (final Observation observation : estimated.getObservations()) {</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outWriter.printf("%d\t%d\t%g\t%s%n", observation.scaledStatistic,</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- estimated.unscale(observation.scaledStatistic), IntArrayList.wrap(observation.covariates));</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try {</span></span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ estimated = load(filename);</span></span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String statName = estimated.getStatAdaptor().statName();</span></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;">+ outWriter.println("tscaled-" + statName + "\t" + statName + "\tcovariates\n");</span></span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (final Observation observation : estimated.getObservations()) {</span></span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outWriter.printf("%d\t%d\t%g\t%s%n", observation.scaledStatistic,</span></span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ estimated.unscale(observation.scaledStatistic), IntArrayList.wrap(observation.covariates));</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="168" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outWriter.close();</span></span>
</pre>
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<td class="diff-line-num new new_line" 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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } catch (ClassNotFoundException e) {</span></span>
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<td class="diff-line-num new new_line" 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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ e.printStackTrace();</span></span>
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<td class="diff-line-num new new_line" 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="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.exit(1);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="172" 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">
172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="173" 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">
173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outWriter.close();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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">
174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } catch (ClassNotFoundException e) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="175" 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">
175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- e.printStackTrace();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="176" 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">
176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.exit(1);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="177" 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">
177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="178" 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">
178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } catch (ParseException e) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="179" 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">
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;">+ System.out.println(e.getMessage());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="180" 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">
180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.exit(1);</span></span>
</pre>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> }</span>
</pre>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> }</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="183" 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">
183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="184" 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">
184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/cli/FoldChangeForExonPairs.java</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="185" 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">
185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/cli/FoldChangeForExonPairs.java</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="186" 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">
186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="187" 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">
187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> package org.campagnelab.goby.cli;</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="188" 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">
188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> </span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="189" 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">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> import edu.cornell.med.icb.io.TSVReader;</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="190" 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">
190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import edu.mssm.crover.cli.CLI;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="191" 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">
191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.apache.commons.cli.*;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="192" 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">
192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> </span>
</pre>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> import java.io.FileReader;</span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> import java.io.FileNotFoundException;</span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="p">@@ -46,38 +46,109 @@</span></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>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"> private void process(String[] args) throws FileNotFoundException {</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String inputFilenames = CLI.getOption(args, "--data", "expression-data.tsv,expression-data2.tsv");</span></span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String pairsFilename = CLI.getOption(args, "--pairs", "pairs.tsv");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="201" 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">
201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String log2AverageId = CLI.getOption(args, "--group", "average log2_RPKM group UHR(BUQ)");</span></span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String outputFilename = CLI.getOption(args, "--output", "/data/gc-weights/exons/out.tsv");</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String averageCountId = CLI.getOption(args, "--threshold-id", "average count group Brain");</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int thresholdValue = CLI.getIntOption(args, "--threshold-value", 20);</span></span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- // String groupB= CLI.getOption(args,"-2","average RPKM group UHR(BUQ)");</span></span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int log2AverageColumnIndex = -1;</span></span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Object2DoubleMap<MutableString> exonExpressionData;</span></span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- ObjectArrayList<Pair> pairs = loadPairs(pairsFilename);</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PrintWriter output = new PrintWriter(outputFilename);</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- output.printf("experiment\texonId1\texonId2\tlog2RpkmExon1-log2RpkmExon2%n");</span></span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (String inputFilename : inputFilenames.split("[,]")) {</span></span>
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215
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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216
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println("Processing " + inputFilename);</span></span>
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217
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- exonExpressionData = loadData(inputFilename, log2AverageId, averageCountId, thresholdValue);</span></span>
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218
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println("Size: " + exonExpressionData.size());</span></span>
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219
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println("Writing data..");</span></span>
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220
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (Pair pair : pairs) {</span></span>
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221
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- //calculate log2 RPKM exonId1 - exonId2:</span></span>
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222
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (exonExpressionData.containsKey(pair.exonId1) && exonExpressionData.containsKey(pair.exonId2)) {</span></span>
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223
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- double log2FoldChangeExons = exonExpressionData.get(pair.exonId1) - exonExpressionData.get(pair.exonId2);</span></span>
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224
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- output.printf("%s\t%s\t%s\t%g%n", FilenameUtils.getBaseName(inputFilename),</span></span>
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225
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- pair.exonId1, pair.exonId2, log2FoldChangeExons);</span></span>
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226
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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227
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Options options = new Options();</span></span>
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228
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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229
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oData = new Option("data", "data", true, "data");</span></span>
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230
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oData.setRequired(false);</span></span>
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231
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oData);</span></span>
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232
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<pre style="margin: 0;">+<span id="LC232" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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233
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<pre style="margin: 0;">+<span id="LC233" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oPairs = new Option("pairs", "pairs", true, "pairs");</span></span>
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234
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oPairs.setRequired(false);</span></span>
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235
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oPairs);</span></span>
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236
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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237
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oGroup = new Option("group", "group", true, "group");</span></span>
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238
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<pre style="margin: 0;">+<span id="LC238" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oGroup.setRequired(false);</span></span>
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239
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<pre style="margin: 0;">+<span id="LC239" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oGroup);</span></span>
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240
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="241" 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">
241
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oOutput = new Option("output", "output", true, "output");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="242" 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">
242
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oOutput.setRequired(false);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="243" 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">
243
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oOutput);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="244" 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">
244
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="245" 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">
245
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oThresId = new Option("thresholdId", "threshold-id", true, "threshold id");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="246" 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">
246
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oThresId.setRequired(false);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="247" 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">
247
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oThresId);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="248" 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">
248
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="249" 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">
249
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<pre style="margin: 0;">+<span id="LC249" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oThresVal = new Option("thresholdVal", "threshold-value", true, "threshold value");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="250" 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">
250
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<pre style="margin: 0;">+<span id="LC250" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oThresVal.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="251" 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">
251
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<pre style="margin: 0;">+<span id="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oThresVal);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="252" 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">
252
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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253
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommandLineParser parser = new DefaultParser();</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="254" 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">
254
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<pre style="margin: 0;">+<span id="LC254" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommandLine cmd;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="255" 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">
255
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<pre style="margin: 0;">+<span id="LC255" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String inputFilenames;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="256" 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">
256
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String pairsFilename;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="257" 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">
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;">+ String log2AverageId;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="258" 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">
258
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String outputFilename;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="259" 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">
259
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String averageCountId;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="260" 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">
260
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int thresholdValue;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="261" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
261
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="262" 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">
262
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="263" 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">
263
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<pre style="margin: 0;">+<span id="LC263" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd = parser.parse(options, args);</span></span>
</pre>
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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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<td class="diff-line-num new new_line" data-linenumber="265" 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">
265
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("data")) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="266" 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">
266
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ inputFilenames = cmd.getOptionValue("data");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="267" 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">
267
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="268" 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">
268
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="269" 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">
269
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ inputFilenames = new String("expression-data.tsv,expression-data2.tsv");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="270" 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">
270
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<pre style="margin: 0;">+<span id="LC270" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="271" 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">
271
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<pre style="margin: 0;">+<span id="LC271" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("pairs")) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="272" 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">
272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pairsFilename = cmd.getOptionValue("pairs");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="273" 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">
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;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="274" 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">
274
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="275" 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">
275
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<pre style="margin: 0;">+<span id="LC275" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pairsFilename = new String("pairs.tsv");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="276" 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">
276
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<pre style="margin: 0;">+<span id="LC276" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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277
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("group")) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="278" 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">
278
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ log2AverageId = cmd.getOptionValue("group");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="279" 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">
279
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="280" 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">
280
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="281" 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">
281
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ log2AverageId = new String("average log2_RPKM group UHR(BUQ)");</span></span>
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282
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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283
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("output")) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="284" 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">
284
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outputFilename = cmd.getOptionValue("output");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="285" 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">
285
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<pre style="margin: 0;">+<span id="LC285" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="286" 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">
286
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<pre style="margin: 0;">+<span id="LC286" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="287" 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">
287
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outputFilename = new String("/data/gc-weights/exons/out.tsv");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="288" 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">
288
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<pre style="margin: 0;">+<span id="LC288" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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289
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<pre style="margin: 0;">+<span id="LC289" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("thresholdId")) {</span></span>
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290
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ averageCountId = cmd.getOptionValue("thresholdId");</span></span>
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291
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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292
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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293
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ averageCountId = new String("average count group Brain");</span></span>
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294
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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295
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("thresholdVal")) {</span></span>
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296
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ thresholdValue = Integer.parseInt(cmd.getOptionValue("thresholdVal"));</span></span>
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297
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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298
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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299
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<pre style="margin: 0;">+<span id="LC299" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ thresholdValue = 20;</span></span>
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300
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"> }</span>
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301
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<pre style="margin: 0;">+<span id="LC301" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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302
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<pre style="margin: 0;">+<span id="LC302" class="line" lang="diff"> </span>
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303
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // String groupB= CLI.getOption(args,"-2","average RPKM group UHR(BUQ)");</span></span>
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304
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int log2AverageColumnIndex = -1;</span></span>
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305
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Object2DoubleMap<MutableString> exonExpressionData;</span></span>
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306
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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307
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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308
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ ObjectArrayList<Pair> pairs = loadPairs(pairsFilename);</span></span>
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309
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PrintWriter output = new PrintWriter(outputFilename);</span></span>
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310
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ output.printf("experiment\texonId1\texonId2\tlog2RpkmExon1-log2RpkmExon2%n");</span></span>
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311
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (String inputFilename : inputFilenames.split("[,]")) {</span></span>
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312
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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313
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.out.println("Processing " + inputFilename);</span></span>
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314
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<pre style="margin: 0;">+<span id="LC314" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ exonExpressionData = loadData(inputFilename, log2AverageId, averageCountId, thresholdValue);</span></span>
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315
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<pre style="margin: 0;">+<span id="LC315" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.out.println("Size: " + exonExpressionData.size());</span></span>
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316
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.out.println("Writing data..");</span></span>
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317
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (Pair pair : pairs) {</span></span>
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318
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //calculate log2 RPKM exonId1 - exonId2:</span></span>
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319
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (exonExpressionData.containsKey(pair.exonId1) && exonExpressionData.containsKey(pair.exonId2)) {</span></span>
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320
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ double log2FoldChangeExons = exonExpressionData.get(pair.exonId1) - exonExpressionData.get(pair.exonId2);</span></span>
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321
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ output.printf("%s\t%s\t%s\t%g%n", FilenameUtils.getBaseName(inputFilename),</span></span>
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322
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ pair.exonId1, pair.exonId2, log2FoldChangeExons);</span></span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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325
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<pre style="margin: 0;">+<span id="LC325" 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="LC326" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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327
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<pre style="margin: 0;">+<span id="LC327" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } catch (ParseException e) {</span></span>
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<pre style="margin: 0;">+<span id="LC328" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.out.println(e.getMessage());</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.exit(1);</span></span>
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<pre style="margin: 0;">+<span id="LC330" 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="LC331" class="line" lang="diff"> }</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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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> private ObjectArrayList<Pair> loadPairs(String pairsFilename) throws FileNotFoundException {</span>
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334
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java</span></span>
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335
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/cli/PlantIndels.java</span></span>
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336
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="p">@@ -19,7 +19,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"> package org.campagnelab.goby.cli;</span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"> import org.campagnelab.goby.parsers.FastaParser;</span>
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<pre style="margin: 0;">+<span id="LC340" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import edu.mssm.crover.cli.CLI;</span></span>
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<pre style="margin: 0;">+<span id="LC341" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.apache.commons.cli.*;</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> import it.unimi.dsi.lang.MutableString;</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> import java.io.*;</span>
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<pre style="margin: 0;">+<span id="LC345" class="line" lang="diff"><span class="p">@@ -40,26 +40,128 @@</span></span>
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<pre style="margin: 0;">+<span id="LC346" class="line" lang="diff"> private int numIndels;</span>
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<pre style="margin: 0;">+<span id="LC347" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC348" class="line" lang="diff"> public static void main(final String args[]) throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC349" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final String fastaReference = CLI.getOption(args, "-r", null);</span></span>
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<pre style="margin: 0;">+<span id="LC350" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final String outputFilename = CLI.getOption(args, "-o", "out.fq");</span></span>
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<pre style="margin: 0;">+<span id="LC351" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final String regionIndelTruth = CLI.getOption(args, "-t", "indel-truth.tsv");</span></span>
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<pre style="margin: 0;">+<span id="LC352" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- // reference sequence to use</span></span>
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<pre style="margin: 0;">+<span id="LC353" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final String refChoice = CLI.getOption(args, "-c", "22");</span></span>
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<pre style="margin: 0;">+<span id="LC354" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int from = CLI.getIntOption(args, "-s", 0);</span></span>
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355
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<pre style="margin: 0;">+<span id="LC355" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int to = CLI.getIntOption(args, "-e", 0);</span></span>
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<pre style="margin: 0;">+<span id="LC356" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC357" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (to < from) {</span></span>
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<pre style="margin: 0;">+<span id="LC358" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.err.println("argument to -e must be larger than argument to -s");</span></span>
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359
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<pre style="margin: 0;">+<span id="LC359" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.exit(1);</span></span>
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360
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<pre style="margin: 0;">+<span id="LC360" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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361
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<pre style="margin: 0;">+<span id="LC361" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final int indelLength = CLI.getIntOption(args, "-l", 3);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="362" 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">
362
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<pre style="margin: 0;">+<span id="LC362" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Options options = new Options();</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="363" 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">
363
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<pre style="margin: 0;">+<span id="LC363" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="364" 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">
364
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<pre style="margin: 0;">+<span id="LC364" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oR = new Option("r", "r", true, "r");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="365" 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">
365
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<pre style="margin: 0;">+<span id="LC365" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oR.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="366" 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">
366
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC366" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oR);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="367" 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">
367
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<pre style="margin: 0;">+<span id="LC367" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="368" 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">
368
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<pre style="margin: 0;">+<span id="LC368" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oO = new Option("o", "o", true, "o");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="369" 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">
369
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<pre style="margin: 0;">+<span id="LC369" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oO.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="370" 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">
370
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC370" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oO);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="371" 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">
371
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<pre style="margin: 0;">+<span id="LC371" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="372" 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">
372
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<pre style="margin: 0;">+<span id="LC372" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oT = new Option("t", "t", true, "t");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="373" 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">
373
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC373" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oT.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="374" 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">
374
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC374" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oT);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="375" 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">
375
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC375" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="376" 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">
376
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC376" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oC = new Option("c", "c", true, "c");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="377" 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">
377
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC377" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oC.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="378" 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">
378
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC378" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oC);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="379" 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">
379
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC379" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="380" 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">
380
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC380" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oS = new Option("s", "s", true, "s");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="381" 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">
381
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC381" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oS.setRequired(false);</span></span>
</pre>
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</tr>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="382" 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">
382
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC382" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oS);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="383" 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">
383
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC383" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="384" 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">
384
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC384" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oE = new Option("e", "e", true, "e");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="385" 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">
385
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC385" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oE.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="386" 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">
386
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<pre style="margin: 0;">+<span id="LC386" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oE);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="387" 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">
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;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="388" 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">
388
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<pre style="margin: 0;">+<span id="LC388" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oL = new Option("l", "l", true, "l");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="389" 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">
389
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<pre style="margin: 0;">+<span id="LC389" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oL.setRequired(false);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="390" 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">
390
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<pre style="margin: 0;">+<span id="LC390" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oL);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="391" 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">
391
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<pre style="margin: 0;">+<span id="LC391" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="392" 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">
392
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<pre style="margin: 0;">+<span id="LC392" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oM = new Option("m", "m", true, "m");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="393" 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">
393
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<pre style="margin: 0;">+<span id="LC393" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oM.setRequired(false);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="394" 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">
394
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<pre style="margin: 0;">+<span id="LC394" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oM);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="395" 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">
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;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="396" 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">
396
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<pre style="margin: 0;">+<span id="LC396" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oRd = new Option("readDeletion", "read-deletion", false, "readDeletion");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="397" 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">
397
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<pre style="margin: 0;">+<span id="LC397" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oRd.setRequired(false);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="398" 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">
398
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<pre style="margin: 0;">+<span id="LC398" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oRd);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="399" 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">
399
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<pre style="margin: 0;">+<span id="LC399" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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400
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<pre style="margin: 0;">+<span id="LC400" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oN = new Option("n", "n", true, "n");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="401" 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">
401
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<pre style="margin: 0;">+<span id="LC401" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oN.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="402" 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">
402
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<pre style="margin: 0;">+<span id="LC402" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oN);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="403" 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">
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;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="404" 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">
404
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<pre style="margin: 0;">+<span id="LC404" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommandLineParser parser = new DefaultParser();</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="405" 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">
405
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<pre style="margin: 0;">+<span id="LC405" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommandLine cmd;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="406" 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">
406
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<pre style="margin: 0;">+<span id="LC406" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final String fastaReference;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="407" 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">
407
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<pre style="margin: 0;">+<span id="LC407" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final String outputFilename;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="408" 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">
408
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<pre style="margin: 0;">+<span id="LC408" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final String regionIndelTruth;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="409" 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">
409
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<pre style="margin: 0;">+<span id="LC409" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // reference sequence to use</span></span>
</pre>
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410
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<pre style="margin: 0;">+<span id="LC410" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final String refChoice;</span></span>
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411
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<pre style="margin: 0;">+<span id="LC411" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int from;</span></span>
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412
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<pre style="margin: 0;">+<span id="LC412" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int to;</span></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;">+ final int indelLength;</span></span>
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414
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<pre style="margin: 0;">+<span id="LC414" class="line" lang="diff"> PlantIndels processor = new PlantIndels();</span>
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415
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<pre style="margin: 0;">+<span id="LC415" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- processor.outputFilename = outputFilename;</span></span>
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416
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<pre style="margin: 0;">+<span id="LC416" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- processor.insert = !CLI.isKeywordGiven(args, "--read-deletion");</span></span>
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417
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<pre style="margin: 0;">+<span id="LC417" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- processor.numIndels=CLI.getIntOption(args,"-n",5);</span></span>
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418
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<pre style="margin: 0;">+<span id="LC418" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- processor.process(refChoice, fastaReference, from, to, indelLength, regionIndelTruth);</span></span>
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419
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<pre style="margin: 0;">+<span id="LC419" class="line" lang="diff"> </span>
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420
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<pre style="margin: 0;">+<span id="LC420" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try {</span></span>
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421
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<pre style="margin: 0;">+<span id="LC421" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd = parser.parse(options, args);</span></span>
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422
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<pre style="margin: 0;">+<span id="LC422" class="line" lang="diff"> </span>
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423
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<pre style="margin: 0;">+<span id="LC423" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("r")) {</span></span>
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424
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<pre style="margin: 0;">+<span id="LC424" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fastaReference = cmd.getOptionValue("r");</span></span>
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425
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<pre style="margin: 0;">+<span id="LC425" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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426
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<pre style="margin: 0;">+<span id="LC426" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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427
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<pre style="margin: 0;">+<span id="LC427" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fastaReference = null;</span></span>
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428
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<pre style="margin: 0;">+<span id="LC428" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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429
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<pre style="margin: 0;">+<span id="LC429" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("o")) {</span></span>
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430
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<pre style="margin: 0;">+<span id="LC430" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outputFilename = cmd.getOptionValue("o");</span></span>
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431
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<pre style="margin: 0;">+<span id="LC431" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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432
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<pre style="margin: 0;">+<span id="LC432" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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433
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<pre style="margin: 0;">+<span id="LC433" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outputFilename = new String("out.fq");</span></span>
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<pre style="margin: 0;">+<span id="LC434" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="435" 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">
435
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<pre style="margin: 0;">+<span id="LC435" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("t")) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="436" 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">
436
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<pre style="margin: 0;">+<span id="LC436" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ regionIndelTruth = cmd.getOptionValue("t");</span></span>
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437
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<pre style="margin: 0;">+<span id="LC437" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="438" 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">
438
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<pre style="margin: 0;">+<span id="LC438" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="439" 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">
439
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<pre style="margin: 0;">+<span id="LC439" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ regionIndelTruth = new String("indel-truth.tsv");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="440" 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">
440
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<pre style="margin: 0;">+<span id="LC440" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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441
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<pre style="margin: 0;">+<span id="LC441" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("c")) {</span></span>
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442
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<pre style="margin: 0;">+<span id="LC442" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ refChoice = cmd.getOptionValue("c");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="443" 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">
443
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<pre style="margin: 0;">+<span id="LC443" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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444
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<pre style="margin: 0;">+<span id="LC444" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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445
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<pre style="margin: 0;">+<span id="LC445" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ refChoice = new String("22");</span></span>
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446
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<pre style="margin: 0;">+<span id="LC446" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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447
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<pre style="margin: 0;">+<span id="LC447" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("s")) {</span></span>
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448
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<pre style="margin: 0;">+<span id="LC448" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from = Integer.parseInt(cmd.getOptionValue("s"));</span></span>
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449
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<pre style="margin: 0;">+<span id="LC449" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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450
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<pre style="margin: 0;">+<span id="LC450" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="451" 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">
451
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<pre style="margin: 0;">+<span id="LC451" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from = 0;</span></span>
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452
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<pre style="margin: 0;">+<span id="LC452" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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453
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<pre style="margin: 0;">+<span id="LC453" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("e")) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="454" 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">
454
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<pre style="margin: 0;">+<span id="LC454" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ to = Integer.parseInt(cmd.getOptionValue("e"));</span></span>
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455
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<pre style="margin: 0;">+<span id="LC455" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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456
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<pre style="margin: 0;">+<span id="LC456" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="457" 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">
457
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<pre style="margin: 0;">+<span id="LC457" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ to = 0;</span></span>
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458
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<pre style="margin: 0;">+<span id="LC458" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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459
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<pre style="margin: 0;">+<span id="LC459" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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460
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<pre style="margin: 0;">+<span id="LC460" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (to < from) {</span></span>
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461
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<pre style="margin: 0;">+<span id="LC461" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.err.println("argument to -e must be larger than argument to -s");</span></span>
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462
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<pre style="margin: 0;">+<span id="LC462" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.exit(1);</span></span>
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463
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<pre style="margin: 0;">+<span id="LC463" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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464
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<pre style="margin: 0;">+<span id="LC464" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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465
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<pre style="margin: 0;">+<span id="LC465" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("l")) {</span></span>
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466
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<pre style="margin: 0;">+<span id="LC466" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ indelLength = Integer.parseInt(cmd.getOptionValue("l"));</span></span>
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467
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<pre style="margin: 0;">+<span id="LC467" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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468
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<pre style="margin: 0;">+<span id="LC468" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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469
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<pre style="margin: 0;">+<span id="LC469" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ indelLength = 3;</span></span>
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470
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<pre style="margin: 0;">+<span id="LC470" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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471
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<pre style="margin: 0;">+<span id="LC471" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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472
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<pre style="margin: 0;">+<span id="LC472" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ processor.outputFilename = outputFilename;</span></span>
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473
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<pre style="margin: 0;">+<span id="LC473" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ processor.insert = !cmd.hasOption("readDeletion");</span></span>
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474
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<pre style="margin: 0;">+<span id="LC474" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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475
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<pre style="margin: 0;">+<span id="LC475" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("n")) {</span></span>
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476
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<pre style="margin: 0;">+<span id="LC476" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ processor.numIndels = Integer.parseInt(cmd.getOptionValue("n"));</span></span>
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477
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<pre style="margin: 0;">+<span id="LC477" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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478
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<pre style="margin: 0;">+<span id="LC478" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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479
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<pre style="margin: 0;">+<span id="LC479" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ processor.numIndels = 5;</span></span>
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480
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<pre style="margin: 0;">+<span id="LC480" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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481
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<pre style="margin: 0;">+<span id="LC481" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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482
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<pre style="margin: 0;">+<span id="LC482" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ processor.process(refChoice, fastaReference, from, to, indelLength, regionIndelTruth);</span></span>
</pre>
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483
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<pre style="margin: 0;">+<span id="LC483" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } catch (ParseException e) {</span></span>
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484
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<pre style="margin: 0;">+<span id="LC484" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.out.println(e.getMessage());</span></span>
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485
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<pre style="margin: 0;">+<span id="LC485" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.exit(1);</span></span>
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486
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<pre style="margin: 0;">+<span id="LC486" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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487
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<pre style="margin: 0;">+<span id="LC487" class="line" lang="diff"> }</span>
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488
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<pre style="margin: 0;">+<span id="LC488" class="line" lang="diff"> </span>
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489
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<pre style="margin: 0;">+<span id="LC489" class="line" lang="diff"> public void process(String refChoice, String fastaReference, int from, int to, int indelLength, String regionIndelTruth) throws IOException {</span>
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490
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<pre style="margin: 0;">+<span id="LC490" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/cli/SimulateBisulfiteReads.java</span></span>
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491
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<pre style="margin: 0;">+<span id="LC491" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/cli/SimulateBisulfiteReads.java</span></span>
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492
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<pre style="margin: 0;">+<span id="LC492" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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493
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<pre style="margin: 0;">+<span id="LC493" class="line" lang="diff"> </span>
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494
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<pre style="margin: 0;">+<span id="LC494" class="line" lang="diff"> import org.campagnelab.goby.reads.QualityEncoding;</span>
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495
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<pre style="margin: 0;">+<span id="LC495" class="line" lang="diff"> import org.campagnelab.goby.parsers.FastaParser;</span>
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496
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<pre style="margin: 0;">+<span id="LC496" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import edu.mssm.crover.cli.CLI;</span></span>
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497
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<pre style="margin: 0;">+<span id="LC497" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.apache.commons.cli.*;</span></span>
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498
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<pre style="margin: 0;">+<span id="LC498" class="line" lang="diff"> import it.unimi.dsi.fastutil.doubles.DoubleArrayList;</span>
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499
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<pre style="margin: 0;">+<span id="LC499" class="line" lang="diff"> import it.unimi.dsi.fastutil.doubles.DoubleIterator;</span>
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500
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<pre style="margin: 0;">+<span id="LC500" class="line" lang="diff"> import it.unimi.dsi.fastutil.doubles.DoubleList;</span>
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501
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<pre style="margin: 0;">+<span id="LC501" class="line" lang="diff"><span class="p">@@ -72,32 +72,152 @@</span></span>
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502
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<pre style="margin: 0;">+<span id="LC502" class="line" lang="diff"> </span>
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503
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<pre style="margin: 0;">+<span id="LC503" class="line" lang="diff"> public static void main(String[] args) throws IOException {</span>
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504
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<pre style="margin: 0;">+<span id="LC504" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC505" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String fastaReference = CLI.getOption(args, "-r", null);</span></span>
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506
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<pre style="margin: 0;">+<span id="LC506" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String outputFilename = CLI.getOption(args, "-o", "out.fq");</span></span>
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507
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<pre style="margin: 0;">+<span id="LC507" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String regionTrueRates = CLI.getOption(args, "-t", "true-methylation.tsv");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="508" 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">
508
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<pre style="margin: 0;">+<span id="LC508" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Options options = new Options();</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="509" 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">
509
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<pre style="margin: 0;">+<span id="LC509" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="510" 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">
510
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<pre style="margin: 0;">+<span id="LC510" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oR = new Option("r", "r", true, "r");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="511" 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">
511
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<pre style="margin: 0;">+<span id="LC511" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oR.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="512" 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">
512
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC512" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oR);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="513" 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">
513
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<pre style="margin: 0;">+<span id="LC513" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="514" 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">
514
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<pre style="margin: 0;">+<span id="LC514" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oO = new Option("o", "o", true, "o");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="515" 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">
515
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<pre style="margin: 0;">+<span id="LC515" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oO.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="516" 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">
516
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<pre style="margin: 0;">+<span id="LC516" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oO);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="517" 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">
517
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<pre style="margin: 0;">+<span id="LC517" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="518" 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">
518
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<pre style="margin: 0;">+<span id="LC518" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oT = new Option("t", "t", true, "t");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="519" 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">
519
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC519" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oT.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="520" 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">
520
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC520" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oT);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="521" 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">
521
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<pre style="margin: 0;">+<span id="LC521" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="522" 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">
522
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<pre style="margin: 0;">+<span id="LC522" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oC = new Option("c", "c", true, "c");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="523" 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">
523
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<pre style="margin: 0;">+<span id="LC523" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oC.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="524" 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">
524
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC524" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oC);</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="525" 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">
525
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<pre style="margin: 0;">+<span id="LC525" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="526" 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">
526
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<pre style="margin: 0;">+<span id="LC526" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oS = new Option("s", "s", true, "s");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="527" 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">
527
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<pre style="margin: 0;">+<span id="LC527" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oS.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="528" 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">
528
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC528" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oS);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="529" 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">
529
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<pre style="margin: 0;">+<span id="LC529" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="530" 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">
530
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<pre style="margin: 0;">+<span id="LC530" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oE = new Option("e", "e", true, "e");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="531" 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">
531
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC531" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oE.setRequired(false);</span></span>
</pre>
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</tr>
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<td class="diff-line-num new new_line" data-linenumber="532" 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">
532
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<pre style="margin: 0;">+<span id="LC532" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oE);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="533" 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">
533
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<pre style="margin: 0;">+<span id="LC533" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="534" 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">
534
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<pre style="margin: 0;">+<span id="LC534" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oL = new Option("l", "l", true, "l");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="535" 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">
535
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<pre style="margin: 0;">+<span id="LC535" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oL.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="536" 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">
536
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<pre style="margin: 0;">+<span id="LC536" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oL);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="537" 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">
537
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<pre style="margin: 0;">+<span id="LC537" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="538" 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">
538
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<pre style="margin: 0;">+<span id="LC538" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oM = new Option("m", "m", true, "m");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="539" 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">
539
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<pre style="margin: 0;">+<span id="LC539" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oM.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="540" 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">
540
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<pre style="margin: 0;">+<span id="LC540" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oM);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="541" 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">
541
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<pre style="margin: 0;">+<span id="LC541" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="542" 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">
542
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<pre style="margin: 0;">+<span id="LC542" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oBs = new Option("bisulfite", "bisulfite", false, "bisulfite");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="543" 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">
543
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<pre style="margin: 0;">+<span id="LC543" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oBs.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="544" 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">
544
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<pre style="margin: 0;">+<span id="LC544" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oBs);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="545" 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">
545
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<pre style="margin: 0;">+<span id="LC545" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="546" 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">
546
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<pre style="margin: 0;">+<span id="LC546" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oStrand = new Option("strand", "strand", true, "strand");</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="547" 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">
547
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<pre style="margin: 0;">+<span id="LC547" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oStrand.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<td class="diff-line-num new new_line" data-linenumber="548" 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">
548
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<pre style="margin: 0;">+<span id="LC548" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oStrand);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="549" 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">
549
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<pre style="margin: 0;">+<span id="LC549" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="550" 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">
550
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<pre style="margin: 0;">+<span id="LC550" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oN = new Option("n", "n", true, "n");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="551" 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">
551
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<pre style="margin: 0;">+<span id="LC551" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oN.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="552" 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">
552
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<pre style="margin: 0;">+<span id="LC552" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oN);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="553" 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">
553
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<pre style="margin: 0;">+<span id="LC553" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="554" 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">
554
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<pre style="margin: 0;">+<span id="LC554" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommandLineParser parser = new DefaultParser();</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="555" 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">
555
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<pre style="margin: 0;">+<span id="LC555" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommandLine cmd;</span></span>
</pre>
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556
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<pre style="margin: 0;">+<span id="LC556" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String fastaReference;</span></span>
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557
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<pre style="margin: 0;">+<span id="LC557" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String outputFilename;</span></span>
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558
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<pre style="margin: 0;">+<span id="LC558" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String regionTrueRates;</span></span>
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559
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<pre style="margin: 0;">+<span id="LC559" class="line" lang="diff"> // reference sequence to use</span>
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560
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<pre style="margin: 0;">+<span id="LC560" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String refChoice = CLI.getOption(args, "-c", "22");</span></span>
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561
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<pre style="margin: 0;">+<span id="LC561" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int from = CLI.getIntOption(args, "-s", 0);</span></span>
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562
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<pre style="margin: 0;">+<span id="LC562" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int to = CLI.getIntOption(args, "-e", 0);</span></span>
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563
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<pre style="margin: 0;">+<span id="LC563" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (to < from) {</span></span>
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564
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<pre style="margin: 0;">+<span id="LC564" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.err.println("argument to -e must be larger than argument to -s");</span></span>
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565
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<pre style="margin: 0;">+<span id="LC565" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.exit(1);</span></span>
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566
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<pre style="margin: 0;">+<span id="LC566" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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567
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<pre style="margin: 0;">+<span id="LC567" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- int readLength = CLI.getIntOption(args, "-l", 50);</span></span>
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568
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<pre style="margin: 0;">+<span id="LC568" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String methylationRateFilename = CLI.getOption(args, "-m", "methylation-rates.tsv");</span></span>
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569
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<pre style="margin: 0;">+<span id="LC569" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String refChoice;</span></span>
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570
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<pre style="margin: 0;">+<span id="LC570" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int from;</span></span>
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571
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<pre style="margin: 0;">+<span id="LC571" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int to;</span></span>
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572
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<pre style="margin: 0;">+<span id="LC572" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ int readLength;</span></span>
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573
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<pre style="margin: 0;">+<span id="LC573" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String methylationRateFilename;</span></span>
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574
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<pre style="margin: 0;">+<span id="LC574" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String strandChoice;</span></span>
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575
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<pre style="margin: 0;">+<span id="LC575" class="line" lang="diff"> SimulateBisulfiteReads processor = new SimulateBisulfiteReads();</span>
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576
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<pre style="margin: 0;">+<span id="LC576" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final boolean bisulfite = CLI.isKeywordGiven(args, "--bisulfite");</span></span>
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577
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<pre style="margin: 0;">+<span id="LC577" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String strandChoice = CLI.getOption(args, "--strand", "both");</span></span>
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578
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<pre style="margin: 0;">+<span id="LC578" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final boolean bisulfite;</span></span>
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579
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<pre style="margin: 0;">+<span id="LC579" class="line" lang="diff"> </span>
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<td class="diff-line-num new new_line" data-linenumber="580" 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">
580
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<pre style="margin: 0;">+<span id="LC580" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- processor.configure(bisulfite, strandChoice);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="581" 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">
581
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<pre style="margin: 0;">+<span id="LC581" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- processor.bisulfiteTreatment = bisulfite;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="582" 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">
582
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<pre style="margin: 0;">+<span id="LC582" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- processor.readLength = readLength;</span></span>
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583
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<pre style="margin: 0;">+<span id="LC583" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- processor.outputFilename = outputFilename;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="584" 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">
584
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<pre style="margin: 0;">+<span id="LC584" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- processor.regionTrueRates = regionTrueRates;</span></span>
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585
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<pre style="margin: 0;">+<span id="LC585" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- processor.numRepeats = CLI.getIntOption(args, "-n", 10000);</span></span>
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586
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<pre style="margin: 0;">+<span id="LC586" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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587
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<pre style="margin: 0;">+<span id="LC587" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- processor.process(refChoice, fastaReference, from, to, methylationRateFilename);</span></span>
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588
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<pre style="margin: 0;">+<span id="LC588" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try {</span></span>
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589
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<pre style="margin: 0;">+<span id="LC589" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd = parser.parse(options, args);</span></span>
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590
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<pre style="margin: 0;">+<span id="LC590" class="line" lang="diff"> </span>
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591
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<pre style="margin: 0;">+<span id="LC591" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("r")) {</span></span>
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592
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<pre style="margin: 0;">+<span id="LC592" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fastaReference = cmd.getOptionValue("r");</span></span>
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593
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<pre style="margin: 0;">+<span id="LC593" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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594
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<pre style="margin: 0;">+<span id="LC594" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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595
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<pre style="margin: 0;">+<span id="LC595" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ fastaReference = null;</span></span>
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596
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<pre style="margin: 0;">+<span id="LC596" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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597
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<pre style="margin: 0;">+<span id="LC597" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("o")) {</span></span>
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598
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<pre style="margin: 0;">+<span id="LC598" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outputFilename = cmd.getOptionValue("o");</span></span>
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599
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<pre style="margin: 0;">+<span id="LC599" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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600
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<pre style="margin: 0;">+<span id="LC600" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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601
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<pre style="margin: 0;">+<span id="LC601" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outputFilename = new String("out.fq");</span></span>
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602
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<pre style="margin: 0;">+<span id="LC602" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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603
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<pre style="margin: 0;">+<span id="LC603" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("t")) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="604" 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">
604
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<pre style="margin: 0;">+<span id="LC604" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ regionTrueRates = cmd.getOptionValue("t");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="605" 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">
605
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<pre style="margin: 0;">+<span id="LC605" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="606" 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">
606
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<pre style="margin: 0;">+<span id="LC606" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="607" 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">
607
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<pre style="margin: 0;">+<span id="LC607" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ regionTrueRates = new String("true-methylation.tsv");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="608" 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">
608
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<pre style="margin: 0;">+<span id="LC608" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="609" 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">
609
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<pre style="margin: 0;">+<span id="LC609" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("c")) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="610" 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">
610
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<pre style="margin: 0;">+<span id="LC610" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ refChoice = cmd.getOptionValue("c");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="611" 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">
611
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<pre style="margin: 0;">+<span id="LC611" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="612" 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">
612
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<pre style="margin: 0;">+<span id="LC612" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="613" 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">
613
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<pre style="margin: 0;">+<span id="LC613" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ refChoice = new String("22");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="614" 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">
614
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<pre style="margin: 0;">+<span id="LC614" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="615" 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">
615
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<pre style="margin: 0;">+<span id="LC615" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("s")) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="616" 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">
616
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<pre style="margin: 0;">+<span id="LC616" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from = Integer.parseInt(cmd.getOptionValue("s"));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="617" 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">
617
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<pre style="margin: 0;">+<span id="LC617" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="618" 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">
618
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<pre style="margin: 0;">+<span id="LC618" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="619" 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">
619
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<pre style="margin: 0;">+<span id="LC619" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ from = 0;</span></span>
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620
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<pre style="margin: 0;">+<span id="LC620" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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621
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<pre style="margin: 0;">+<span id="LC621" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("e")) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="622" 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">
622
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<pre style="margin: 0;">+<span id="LC622" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ to = Integer.parseInt(cmd.getOptionValue("e"));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="623" 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">
623
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<pre style="margin: 0;">+<span id="LC623" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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624
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<pre style="margin: 0;">+<span id="LC624" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="625" 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">
625
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<pre style="margin: 0;">+<span id="LC625" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ to = 0;</span></span>
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626
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<pre style="margin: 0;">+<span id="LC626" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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627
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<pre style="margin: 0;">+<span id="LC627" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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628
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<pre style="margin: 0;">+<span id="LC628" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (to < from) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="629" 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">
629
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<pre style="margin: 0;">+<span id="LC629" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.err.println("argument to -e must be larger than argument to -s");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="630" 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">
630
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<pre style="margin: 0;">+<span id="LC630" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.exit(1);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="631" 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">
631
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<pre style="margin: 0;">+<span id="LC631" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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632
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<pre style="margin: 0;">+<span id="LC632" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="633" 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">
633
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<pre style="margin: 0;">+<span id="LC633" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("l")) {</span></span>
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634
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<pre style="margin: 0;">+<span id="LC634" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ readLength = Integer.parseInt(cmd.getOptionValue("l"));</span></span>
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<td class="diff-line-num new new_line" data-linenumber="635" 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">
635
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<pre style="margin: 0;">+<span id="LC635" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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636
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<pre style="margin: 0;">+<span id="LC636" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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637
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<pre style="margin: 0;">+<span id="LC637" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ readLength = 50;</span></span>
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638
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<pre style="margin: 0;">+<span id="LC638" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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639
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<pre style="margin: 0;">+<span id="LC639" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("m")) {</span></span>
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640
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<pre style="margin: 0;">+<span id="LC640" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ methylationRateFilename = cmd.getOptionValue("c");</span></span>
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641
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<pre style="margin: 0;">+<span id="LC641" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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642
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<pre style="margin: 0;">+<span id="LC642" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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643
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<pre style="margin: 0;">+<span id="LC643" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ methylationRateFilename = new String("methylation-rates.tsv");</span></span>
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644
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<pre style="margin: 0;">+<span id="LC644" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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645
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<pre style="margin: 0;">+<span id="LC645" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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646
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<pre style="margin: 0;">+<span id="LC646" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ bisulfite = cmd.hasOption("biSulfite");</span></span>
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647
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<pre style="margin: 0;">+<span id="LC647" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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648
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<pre style="margin: 0;">+<span id="LC648" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("strand")) {</span></span>
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649
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<pre style="margin: 0;">+<span id="LC649" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strandChoice = cmd.getOptionValue("strang");</span></span>
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650
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<pre style="margin: 0;">+<span id="LC650" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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651
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<pre style="margin: 0;">+<span id="LC651" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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652
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<pre style="margin: 0;">+<span id="LC652" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ strandChoice = new String("both");</span></span>
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<pre style="margin: 0;">+<span id="LC653" 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="LC654" 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="LC655" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ processor.configure(bisulfite, strandChoice);</span></span>
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<pre style="margin: 0;">+<span id="LC656" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ processor.bisulfiteTreatment = bisulfite;</span></span>
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<pre style="margin: 0;">+<span id="LC657" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ processor.readLength = readLength;</span></span>
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<pre style="margin: 0;">+<span id="LC658" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ processor.outputFilename = outputFilename;</span></span>
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<pre style="margin: 0;">+<span id="LC659" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ processor.regionTrueRates = regionTrueRates;</span></span>
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<pre style="margin: 0;">+<span id="LC660" 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="LC661" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("n")) {</span></span>
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<pre style="margin: 0;">+<span id="LC662" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ processor.numRepeats = Integer.parseInt(cmd.getOptionValue("n"));</span></span>
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663
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<pre style="margin: 0;">+<span id="LC663" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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664
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<pre style="margin: 0;">+<span id="LC664" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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<pre style="margin: 0;">+<span id="LC665" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ processor.numRepeats = 10000;</span></span>
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<pre style="margin: 0;">+<span id="LC666" 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="LC667" 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="LC668" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ processor.process(refChoice, fastaReference, from, to, methylationRateFilename);</span></span>
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<pre style="margin: 0;">+<span id="LC669" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } catch (ParseException e) {</span></span>
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<pre style="margin: 0;">+<span id="LC670" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.out.println(e.getMessage());</span></span>
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<pre style="margin: 0;">+<span id="LC671" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.exit(1);</span></span>
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<pre style="margin: 0;">+<span id="LC672" 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="LC673" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC674" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC675" class="line" lang="diff"> public void configure(boolean bisulfite, String strandChoice) {</span>
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<pre style="margin: 0;">+<span id="LC676" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/methylation/MethylSimilarityScan.java</span></span>
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677
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<pre style="margin: 0;">+<span id="LC677" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/methylation/MethylSimilarityScan.java</span></span>
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<pre style="margin: 0;">+<span id="LC678" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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679
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<pre style="margin: 0;">+<span id="LC679" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC680" class="line" lang="diff"> import org.campagnelab.goby.cli.DoInParallel;</span>
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681
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<pre style="margin: 0;">+<span id="LC681" class="line" lang="diff"> import edu.cornell.med.icb.io.TSVReader;</span>
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682
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<pre style="margin: 0;">+<span id="LC682" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import edu.mssm.crover.cli.CLI;</span></span>
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683
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<pre style="margin: 0;">+<span id="LC683" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.apache.commons.cli.*;</span></span>
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<pre style="margin: 0;">+<span id="LC684" class="line" lang="diff"> import it.unimi.dsi.fastutil.floats.FloatArrayList;</span>
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685
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<pre style="margin: 0;">+<span id="LC685" class="line" lang="diff"> import it.unimi.dsi.fastutil.ints.*;</span>
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<pre style="margin: 0;">+<span id="LC686" class="line" lang="diff"> import it.unimi.dsi.fastutil.io.BinIO;</span>
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<pre style="margin: 0;">+<span id="LC687" class="line" lang="diff"><span class="p">@@ -63,40 +63,92 @@</span></span>
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<pre style="margin: 0;">+<span id="LC688" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC689" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC690" class="line" lang="diff"> private void process(String[] args) throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC691" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String inputFilename = CLI.getOption(args, "-i", "/data/lister/mc_h1.tsv");</span></span>
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692
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<pre style="margin: 0;">+<span id="LC692" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- this.windowWidths = CLI.getOption(args, "-w", "10");</span></span>
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693
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<pre style="margin: 0;">+<span id="LC693" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- this.maxBestHits = CLI.getIntOption(args, "-h", 100);</span></span>
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694
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<pre style="margin: 0;">+<span id="LC694" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- String outputFilename = CLI.getOption(args, "-o", "out.tsv");</span></span>
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695
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<pre style="margin: 0;">+<span id="LC695" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final MethylationData data = load(inputFilename);</span></span>
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696
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<pre style="margin: 0;">+<span id="LC696" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- File outputFile = new File(outputFilename);</span></span>
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697
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<pre style="margin: 0;">+<span id="LC697" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- boolean outputFileExists = outputFile.exists();</span></span>
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698
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<pre style="margin: 0;">+<span id="LC698" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-// append:</span></span>
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699
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<pre style="margin: 0;">+<span id="LC699" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- PrintWriter output = new PrintWriter(new FileWriter(outputFilename, true));</span></span>
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700
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<pre style="margin: 0;">+<span id="LC700" class="line" lang="diff"> </span>
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701
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<pre style="margin: 0;">+<span id="LC701" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Options options = new Options();</span></span>
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702
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<pre style="margin: 0;">+<span id="LC702" class="line" lang="diff"> </span>
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703
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<pre style="margin: 0;">+<span id="LC703" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (!outputFileExists) {</span></span>
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704
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<pre style="margin: 0;">+<span id="LC704" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- output.write("windowSize\tlocation\tchromosome\tforward strand start\tforward strand end\treverse strand start\treverse strand end\teffective window size\tstatistic\n");</span></span>
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705
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<pre style="margin: 0;">+<span id="LC705" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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706
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<pre style="margin: 0;">+<span id="LC706" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (String windowWidthString : windowWidths.split("[,]")) {</span></span>
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707
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<pre style="margin: 0;">+<span id="LC707" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final int windowWidth = Integer.parseInt(windowWidthString);</span></span>
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708
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<pre style="margin: 0;">+<span id="LC708" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.out.println("Processing window size=" + windowWidth);</span></span>
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709
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<pre style="margin: 0;">+<span id="LC709" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final HitBoundedPriorityQueue hits = new HitBoundedPriorityQueue(maxBestHits);</span></span>
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710
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<pre style="margin: 0;">+<span id="LC710" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- DoInParallel scan = new DoInParallel() {</span></span>
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711
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<pre style="margin: 0;">+<span id="LC711" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @Override</span></span>
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712
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<pre style="margin: 0;">+<span id="LC712" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void action(DoInParallel forDataAccess, String chromosome, int loopIndex) {</span></span>
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713
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<pre style="margin: 0;">+<span id="LC713" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- compareStrands(hits, data, windowWidth, new MutableString(chromosome));</span></span>
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714
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<pre style="margin: 0;">+<span id="LC714" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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715
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<pre style="margin: 0;">+<span id="LC715" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- };</span></span>
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716
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<pre style="margin: 0;">+<span id="LC716" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oI = new Option("i", "i", true, "i");</span></span>
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717
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<pre style="margin: 0;">+<span id="LC717" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oI.setRequired(false);</span></span>
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718
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<pre style="margin: 0;">+<span id="LC718" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oI);</span></span>
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719
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<pre style="margin: 0;">+<span id="LC719" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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720
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<pre style="margin: 0;">+<span id="LC720" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oW = new Option("w", "w", true, "w");</span></span>
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721
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<pre style="margin: 0;">+<span id="LC721" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oW.setRequired(false);</span></span>
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722
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<pre style="margin: 0;">+<span id="LC722" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oW);</span></span>
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723
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<pre style="margin: 0;">+<span id="LC723" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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724
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<pre style="margin: 0;">+<span id="LC724" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oH = new Option("h", "h", true, "h");</span></span>
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725
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<pre style="margin: 0;">+<span id="LC725" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oH.setRequired(false);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="726" 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">
726
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<pre style="margin: 0;">+<span id="LC726" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oH);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="727" 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">
727
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<pre style="margin: 0;">+<span id="LC727" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="728" 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">
728
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<pre style="margin: 0;">+<span id="LC728" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option oO = new Option("o", "o", true, "o");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="729" 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">
729
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<pre style="margin: 0;">+<span id="LC729" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ oO.setRequired(false);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="730" 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">
730
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<pre style="margin: 0;">+<span id="LC730" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(oO);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="731" 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">
731
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<pre style="margin: 0;">+<span id="LC731" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="732" 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">
732
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<pre style="margin: 0;">+<span id="LC732" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommandLineParser parser = new DefaultParser();</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="733" 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">
733
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<pre style="margin: 0;">+<span id="LC733" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommandLine cmd;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="734" 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">
734
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<pre style="margin: 0;">+<span id="LC734" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String inputFilename;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="735" 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">
735
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<pre style="margin: 0;">+<span id="LC735" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ String outputFilename;</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="736" 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">
736
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<pre style="margin: 0;">+<span id="LC736" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="737" 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">
737
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC737" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try {</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="738" 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">
738
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<pre style="margin: 0;">+<span id="LC738" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd = parser.parse(options, args);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="739" 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">
739
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<pre style="margin: 0;">+<span id="LC739" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="740" 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">
740
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC740" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("i")) {</span></span>
</pre>
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<td class="diff-line-num new old_line" data-linenumber="0" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
</td>
<td class="diff-line-num new new_line" data-linenumber="741" 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">
741
</td>
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<pre style="margin: 0;">+<span id="LC741" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ inputFilename = cmd.getOptionValue("i");</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="742" 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">
742
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<pre style="margin: 0;">+<span id="LC742" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="743" 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">
743
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<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC743" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="744" 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">
744
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<pre style="margin: 0;">+<span id="LC744" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ inputFilename = new String("/data/lister/mc_h1.tsv");</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="745" 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">
745
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<pre style="margin: 0;">+<span id="LC745" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="746" 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">
746
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<pre style="margin: 0;">+<span id="LC746" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("w")) {</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="747" 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">
747
</td>
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<pre style="margin: 0;">+<span id="LC747" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ this.windowWidths = cmd.getOptionValue("w");</span></span>
</pre>
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</td>
<td class="diff-line-num new new_line" data-linenumber="748" 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">
748
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC748" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="749" 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">
749
</td>
<td class="line_content new" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC749" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
</pre>
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750
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<pre style="margin: 0;">+<span id="LC750" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ this.windowWidths = new String("10");</span></span>
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751
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<pre style="margin: 0;">+<span id="LC751" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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752
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<pre style="margin: 0;">+<span id="LC752" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("h")) {</span></span>
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753
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<pre style="margin: 0;">+<span id="LC753" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ this.maxBestHits = Integer.parseInt(cmd.getOptionValue("h"));</span></span>
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754
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<pre style="margin: 0;">+<span id="LC754" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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755
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<pre style="margin: 0;">+<span id="LC755" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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756
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<pre style="margin: 0;">+<span id="LC756" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ this.maxBestHits = 100;</span></span>
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757
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<pre style="margin: 0;">+<span id="LC757" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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758
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<pre style="margin: 0;">+<span id="LC758" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("o")) {</span></span>
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759
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<pre style="margin: 0;">+<span id="LC759" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outputFilename = cmd.getOptionValue("o");</span></span>
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760
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<pre style="margin: 0;">+<span id="LC760" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="761" 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">
761
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<pre style="margin: 0;">+<span id="LC761" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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762
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<pre style="margin: 0;">+<span id="LC762" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ outputFilename = new String("out.tsv");</span></span>
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763
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<pre style="margin: 0;">+<span id="LC763" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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764
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<pre style="margin: 0;">+<span id="LC764" class="line" lang="diff"> </span>
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765
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<pre style="margin: 0;">+<span id="LC765" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- try {</span></span>
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766
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<pre style="margin: 0;">+<span id="LC766" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- scan.execute(true, data.getChromosomeStrings());</span></span>
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767
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<pre style="margin: 0;">+<span id="LC767" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } catch (Exception e) {</span></span>
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768
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<pre style="margin: 0;">+<span id="LC768" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.</span></span>
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769
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<pre style="margin: 0;">+<span id="LC769" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final MethylationData data = load(inputFilename);</span></span>
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770
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<pre style="margin: 0;">+<span id="LC770" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ File outputFile = new File(outputFilename);</span></span>
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771
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<pre style="margin: 0;">+<span id="LC771" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ boolean outputFileExists = outputFile.exists();</span></span>
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772
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<pre style="margin: 0;">+<span id="LC772" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ // append:</span></span>
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773
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<pre style="margin: 0;">+<span id="LC773" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ PrintWriter output = new PrintWriter(new FileWriter(outputFilename, true));</span></span>
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<pre style="margin: 0;">+<span id="LC774" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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775
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<pre style="margin: 0;">+<span id="LC775" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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776
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<pre style="margin: 0;">+<span id="LC776" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (!outputFileExists) {</span></span>
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777
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<pre style="margin: 0;">+<span id="LC777" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ output.write("windowSize\tlocation\tchromosome\tforward strand start\tforward strand end\treverse strand start\treverse strand end\teffective window size\tstatistic\n");</span></span>
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778
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<pre style="margin: 0;">+<span id="LC778" class="line" lang="diff"> }</span>
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779
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<pre style="margin: 0;">+<span id="LC779" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ for (String windowWidthString : windowWidths.split("[,]")) {</span></span>
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780
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<pre style="margin: 0;">+<span id="LC780" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final int windowWidth = Integer.parseInt(windowWidthString);</span></span>
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781
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<pre style="margin: 0;">+<span id="LC781" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.out.println("Processing window size=" + windowWidth);</span></span>
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782
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<pre style="margin: 0;">+<span id="LC782" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final HitBoundedPriorityQueue hits = new HitBoundedPriorityQueue(maxBestHits);</span></span>
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783
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<pre style="margin: 0;">+<span id="LC783" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ DoInParallel scan = new DoInParallel() {</span></span>
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784
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<pre style="margin: 0;">+<span id="LC784" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ @Override</span></span>
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785
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<pre style="margin: 0;">+<span id="LC785" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ public void action(DoInParallel forDataAccess, String chromosome, int loopIndex) {</span></span>
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786
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<pre style="margin: 0;">+<span id="LC786" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ compareStrands(hits, data, windowWidth, new MutableString(chromosome));</span></span>
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787
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<pre style="margin: 0;">+<span id="LC787" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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788
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<pre style="margin: 0;">+<span id="LC788" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ };</span></span>
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789
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<pre style="margin: 0;">+<span id="LC789" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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790
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<pre style="margin: 0;">+<span id="LC790" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try {</span></span>
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791
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<pre style="margin: 0;">+<span id="LC791" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ scan.execute(true, data.getChromosomeStrings());</span></span>
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792
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<pre style="margin: 0;">+<span id="LC792" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } catch (Exception e) {</span></span>
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793
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<pre style="margin: 0;">+<span id="LC793" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.</span></span>
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794
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<pre style="margin: 0;">+<span id="LC794" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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795
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<pre style="margin: 0;">+<span id="LC795" class="line" lang="diff"> </span>
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796
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<pre style="margin: 0;">+<span id="LC796" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- printResults(hits, windowWidth, data, output);</span></span>
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797
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<pre style="margin: 0;">+<span id="LC797" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ printResults(hits, windowWidth, data, output);</span></span>
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798
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<pre style="margin: 0;">+<span id="LC798" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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799
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<pre style="margin: 0;">+<span id="LC799" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ output.close();</span></span>
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800
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<pre style="margin: 0;">+<span id="LC800" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } catch (ParseException e) {</span></span>
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801
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<pre style="margin: 0;">+<span id="LC801" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.out.println(e.getMessage());</span></span>
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802
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<pre style="margin: 0;">+<span id="LC802" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.exit(1);</span></span>
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803
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<pre style="margin: 0;">+<span id="LC803" class="line" lang="diff"> }</span>
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804
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<pre style="margin: 0;">+<span id="LC804" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- output.close();</span></span>
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805
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<pre style="margin: 0;">+<span id="LC805" class="line" lang="diff"> }</span>
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806
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<pre style="margin: 0;">+<span id="LC806" class="line" lang="diff"> </span>
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807
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<pre style="margin: 0;">+<span id="LC807" class="line" lang="diff"> </span>
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808
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<pre style="margin: 0;">+<span id="LC808" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java</span></span>
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809
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<pre style="margin: 0;">+<span id="LC809" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/PercentMismatchesQualityFilter.java</span></span>
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<td class="diff-line-num new new_line" data-linenumber="810" 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">
810
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<pre style="margin: 0;">+<span id="LC810" class="line" lang="diff"><span class="p">@@ -20,7 +20,7 @@</span></span>
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811
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<pre style="margin: 0;">+<span id="LC811" class="line" lang="diff"> </span>
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812
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<pre style="margin: 0;">+<span id="LC812" class="line" lang="diff"> package org.campagnelab.goby.modes;</span>
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813
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<pre style="margin: 0;">+<span id="LC813" class="line" lang="diff"> </span>
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814
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<pre style="margin: 0;">+<span id="LC814" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import edu.mssm.crover.cli.CLI;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="815" 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">
815
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<pre style="margin: 0;">+<span id="LC815" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.apache.commons.cli.*;</span></span>
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816
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<pre style="margin: 0;">+<span id="LC816" class="line" lang="diff"> import org.apache.commons.lang.StringUtils;</span>
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817
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<pre style="margin: 0;">+<span id="LC817" class="line" lang="diff"> import org.campagnelab.goby.alignments.Alignments;</span>
</pre>
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818
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<pre style="margin: 0;">+<span id="LC818" class="line" lang="diff"> import org.campagnelab.goby.alignments.filters.AlignmentQualityFilter;</span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="819" 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">
819
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<pre style="margin: 0;">+<span id="LC819" class="line" lang="diff"><span class="p">@@ -62,8 +62,28 @@</span></span>
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820
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<pre style="margin: 0;">+<span id="LC820" class="line" lang="diff"> </span>
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821
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<pre style="margin: 0;">+<span id="LC821" class="line" lang="diff"> public void setParameters(final String parameters) {</span>
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822
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<pre style="margin: 0;">+<span id="LC822" class="line" lang="diff"> final String[] args = StringUtils.defaultString(parameters).split("[',=]");</span>
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<td class="diff-line-num new new_line" data-linenumber="823" 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">
823
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<pre style="margin: 0;">+<span id="LC823" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- qualityThresholdPercent = CLI.getDoubleOption(args, "threshold", 0.05d);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="824" 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">
824
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<pre style="margin: 0;">+<span id="LC824" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- System.err.println("Setting quality threshold to " + qualityThresholdPercent);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="825" 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">
825
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<pre style="margin: 0;">+<span id="LC825" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Options options = new Options();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="826" 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">
826
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<pre style="margin: 0;">+<span id="LC826" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="827" 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">
827
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<pre style="margin: 0;">+<span id="LC827" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ Option threshold = new Option("threshold", "threshold", true, "threshold");</span></span>
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<td class="diff-line-num new new_line" data-linenumber="828" 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">
828
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<pre style="margin: 0;">+<span id="LC828" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ threshold.setRequired(false);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="829" 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">
829
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<pre style="margin: 0;">+<span id="LC829" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addOption(threshold);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="830" 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">
830
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<pre style="margin: 0;">+<span id="LC830" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommandLineParser parser = new DefaultParser();</span></span>
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<td class="diff-line-num new new_line" data-linenumber="831" 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">
831
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<pre style="margin: 0;">+<span id="LC831" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ CommandLine cmd;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="832" 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">
832
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<pre style="margin: 0;">+<span id="LC832" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="833" 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">
833
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<pre style="margin: 0;">+<span id="LC833" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ try {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="834" 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">
834
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<pre style="margin: 0;">+<span id="LC834" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ cmd = parser.parse(options, args);</span></span>
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835
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<pre style="margin: 0;">+<span id="LC835" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="836" 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">
836
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<pre style="margin: 0;">+<span id="LC836" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ if (cmd.hasOption("threshold")) {</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="837" 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">
837
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<pre style="margin: 0;">+<span id="LC837" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ qualityThresholdPercent = Double.parseDouble(cmd.getOptionValue("threshold"));</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="838" 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">
838
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<pre style="margin: 0;">+<span id="LC838" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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<td class="diff-line-num new new_line" data-linenumber="839" 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">
839
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<pre style="margin: 0;">+<span id="LC839" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ else {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="840" 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">
840
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<pre style="margin: 0;">+<span id="LC840" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ qualityThresholdPercent = 0.05d;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="841" 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">
841
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<pre style="margin: 0;">+<span id="LC841" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ }</span></span>
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842
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<pre style="margin: 0;">+<span id="LC842" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.err.println("Setting quality threshold to " + qualityThresholdPercent);</span></span>
</pre>
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<td class="diff-line-num new new_line" data-linenumber="843" 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">
843
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<pre style="margin: 0;">+<span id="LC843" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ } catch (ParseException e) {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="844" 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">
844
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<pre style="margin: 0;">+<span id="LC844" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.out.println(e.getMessage());</span></span>
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845
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<pre style="margin: 0;">+<span id="LC845" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ System.exit(1);</span></span>
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846
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<pre style="margin: 0;">+<span id="LC846" 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="LC847" class="line" lang="diff"> }</span>
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848
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<pre style="margin: 0;">+<span id="LC848" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC849" class="line" lang="diff"> public void printUsage(final PrintStream out) {</span></pre>
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<li id="ef745f5cc2f1850f044372eaa52b7f53ca4cc69f">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#ef745f5cc2f1850f044372eaa52b7f53ca4cc69f"><strong>debian/patches/using_correct_SamReader_api.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Description: using the correct SamReader api</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Author: Pierre Gruet <pgtdebian@free.fr></span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Origin: https://sources.debian.org/src/fastqc/0.11.9+dfsg-4/debian/patches/htsjdk-api.patch</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"><span class="p">Forwarded: no</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="p">Last-Update: 2020-11-06</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMComparisonMode.java</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMComparisonMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="p">@@ -32,9 +32,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> import org.campagnelab.goby.util.dynoptions.RegisterThis;</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> import htsjdk.samtools.ValidationStringency;</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> import it.unimi.dsi.logging.ProgressLogger;</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import htsjdk.samtools.SAMFileReader;</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import htsjdk.samtools.SAMRecord;</span></span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import htsjdk.samtools.SAMRecordIterator;</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;">+import htsjdk.samtools.*;</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> import org.slf4j.Logger;</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> import org.slf4j.LoggerFactory;</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="p">@@ -284,12 +282,15 @@</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> }</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"> System.out.println("Comparing source bam and destination bam");</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader sourceParser = new SAMFileReader(new FileInputStream(sourceBamFile));</span></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;">- final SAMFileReader destParser = new SAMFileReader(new FileInputStream(destBamFile));</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;">+ final SamInputResource sirSource = SamInputResource.of(new FileInputStream(sourceBamFile));</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;">+ final SamReaderFactory srfSource = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</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 SamInputResource sirDest = SamInputResource.of(new FileInputStream(destBamFile));</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;">+ final SamReaderFactory srfDest = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</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;">+</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader sourceParser = srfSource.open(sirSource);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader destParser = srfDest.open(sirDest);</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> // We need to set the validation to silent because an incomplete file (if the source isn't the entire file)</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"> // we can see errors that wouldn't exist in a real conversion.</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;">- sourceParser.setValidationStringency(ValidationStringency.SILENT);</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;">- destParser.setValidationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> final SAMRecordIterator sourceIterator = sourceParser.iterator();</span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> final SAMRecordIterator destIterator = destParser.iterator();</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> AlignmentReaderImpl gobyReader = null;</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactMode.java</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;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="p">@@ -242,10 +242,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> final ProgressLogger progress = new ProgressLogger(LOG);</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> progress.displayFreeMemory = true;</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> // the following is required to set validation to SILENT before loading the header (done in the SAMFileReader constructor)</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);</span></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;">-</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> final InputStream stream = "-".equals(inputFile) ? System.in : new FileInputStream(inputFile);</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(stream);</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;">+ final SamInputResource sir = SamInputResource.of(stream);</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;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC52" 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="LC53" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> // transfer read groups to Goby header:</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> final SAMFileHeader samHeader = parser.getFileHeader();</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> final IndexedIdentifier readGroups = new IndexedIdentifier();</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactOldMode.java</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;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactOldMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="p">@@ -128,8 +128,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> final int[] readLengths = createReadLengthArray();</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"> final ProgressLogger progress = new ProgressLogger(LOG);</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;">- final SAMFileReader parser = new SAMFileReader(new File(inputFile));</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;">- parser.setValidationStringency(ValidationStringency.SILENT);</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;">+ final SamInputResource sir = SamInputResource.of(new File(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC67" 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="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></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"> progress.start();</span>
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> </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;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SAMToCompactSamHelperMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="p">@@ -231,10 +231,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> final ProgressLogger progress = new ProgressLogger(LOG);</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> progress.displayFreeMemory = true;</span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> // the following is required to set validation to SILENT before loading the header (done in the SAMFileReader constructor)</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);</span></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;">-</span></span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> final InputStream stream = "-".equals(inputFile) ? System.in : new FileInputStream(inputFile);</span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(stream);</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;">+ final SamInputResource sir = SamInputResource.of(stream);</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;">+ SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</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;">+</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;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> // transfer read groups to Goby header:</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> final SAMFileHeader samHeader = parser.getFileHeader();</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> final IndexedIdentifier readGroups = new IndexedIdentifier();</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="p">@@ -827,4 +828,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC93" 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="LC94" 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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<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 class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SamExtractReadsMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="p">@@ -30,8 +30,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> import htsjdk.samtools.ValidationStringency;</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> import it.unimi.dsi.lang.MutableString;</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> import it.unimi.dsi.logging.ProgressLogger;</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import htsjdk.samtools.SAMFileReader;</span></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;">-import htsjdk.samtools.SAMRecord;</span></span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.*;</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> import org.slf4j.Logger;</span>
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> import org.slf4j.LoggerFactory;</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"><span class="p">@@ -142,8 +141,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> try {</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> final ProgressLogger progress = new ProgressLogger(LOG);</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> // the following is required to set validation to SILENT before loading the header (done in the SAMFileReader constructor)</span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(new File(inputFilename), null);</span></span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamInputResource sir = SamInputResource.of(new File(inputFilename));</span></span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC116" 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="LC117" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> progress.start();</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/modes/SampleQualityScoresMode.java</span></span>
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="p">@@ -29,8 +29,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> import it.unimi.dsi.fastutil.ints.IntArrayList;</span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> import it.unimi.dsi.fastutil.ints.IntList;</span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> import it.unimi.dsi.lang.MutableString;</span>
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import htsjdk.samtools.SAMFileReader;</span></span>
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import htsjdk.samtools.SAMRecord;</span></span>
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.*;</span></span>
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> import org.apache.commons.lang.ArrayUtils;</span>
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> import org.apache.commons.logging.Log;</span>
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> import org.apache.commons.logging.LogFactory;</span>
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="p">@@ -350,8 +349,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> private int processSamReadsFile(final String inputFilename) throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> // Create directory for output file if it doesn't already exist</span>
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> int i = 0;</span>
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- SAMFileReader.setDefaultValidationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFilename));</span></span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFilename));</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" 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="LC142" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {</span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"> final String quality = samRecord.getBaseQualityString();</span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> if (quality != null && quality.length() != 0) {</span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/RoundTripAlignment.java</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/test/java/org/campagnelab/goby/readers/sam/RoundTripAlignment.java</span></span>
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="p">@@ -32,9 +32,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"> import org.campagnelab.goby.reads.RandomAccessSequenceTestSupport;</span>
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> import htsjdk.samtools.ValidationStringency;</span>
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> import it.unimi.dsi.logging.ProgressLogger;</span>
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import htsjdk.samtools.SAMFileReader;</span></span>
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import htsjdk.samtools.SAMRecord;</span></span>
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import htsjdk.samtools.SAMRecordIterator;</span></span>
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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 htsjdk.samtools.*;</span></span>
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> import org.apache.commons.io.FilenameUtils;</span>
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"> import org.slf4j.Logger;</span>
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"> import org.slf4j.LoggerFactory;</span>
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"><span class="p">@@ -172,12 +170,15 @@</span></span>
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> LOG.info("Comparing source bam and destination bam");</span>
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader sourceParser = new SAMFileReader(new FileInputStream(sourceBamFilename));</span></span>
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader destParser = new SAMFileReader(new FileInputStream(destBamFilename));</span></span>
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamInputResource sirSource = SamInputResource.of(new FileInputStream(sourceBamFilename));</span></span>
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srfSource = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamInputResource sirDest = SamInputResource.of(new FileInputStream(destBamFilename));</span></span>
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srfDest = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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169
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<pre style="margin: 0;">+<span id="LC169" 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="LC170" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader sourceParser = srfSource.open(sirSource);</span></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;">+ final SamReader destParser = srfDest.open(sirDest);</span></span>
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> // We need to set the validation to silent because an incomplete file (if the source isn't the entire file)</span>
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> // we can see errors that wouldn't exist in a real conversion.</span>
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<td class="diff-line-num new new_line" data-linenumber="174" 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="LC174" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- sourceParser.setValidationStringency(ValidationStringency.SILENT);</span></span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- destParser.setValidationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"> final SAMRecordIterator sourceIterator = sourceParser.iterator();</span>
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> final SAMRecordIterator destIterator = destParser.iterator();</span>
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> AlignmentReaderImpl gobyReader = null;</span>
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<pre style="margin: 0;">+<span id="LC179" 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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<pre style="margin: 0;">+<span id="LC180" 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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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"><span class="p">@@ -25,8 +25,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> import htsjdk.samtools.ValidationStringency;</span>
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> import it.unimi.dsi.lang.MutableString;</span>
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"> import junit.framework.Assert;</span>
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import htsjdk.samtools.SAMFileReader;</span></span>
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import htsjdk.samtools.SAMRecord;</span></span>
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import htsjdk.samtools.*;</span></span>
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> import org.apache.commons.io.FilenameUtils;</span>
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"> import org.slf4j.Logger;</span>
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> import org.junit.BeforeClass;</span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"><span class="p">@@ -65,8 +64,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> // like 9 no genome</span>
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"> public void testSamToCompactTrickCase9NoGenome() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"> final String inputFile = "test-data/splicedsamhelper/tricky-spliced-9.sam";</span>
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));</span></span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- parser.setValidationStringency(ValidationStringency.SILENT);</span></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;">+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));</span></span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC199" 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="LC200" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> final SamRecordParser recordParser = new SamRecordParser();</span>
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"> for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {</span>
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"><span class="p">@@ -84,8 +85,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> public void testSamToCompactTrickCase10NoGenome() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"> final String inputFile = "test-data/splicedsamhelper/tricky-spliced-10.sam";</span>
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- parser.setValidationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC212" 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="LC213" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> final SamRecordParser recordParser = new SamRecordParser();</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="p">@@ -103,8 +106,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> public void testSamToCompactTrickCase11() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> final String inputFile = "test-data/splicedsamhelper/tricky-spliced-11.sam";</span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- parser.setValidationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC225" 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="LC226" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> final SamRecordParser recordParser = new SamRecordParser();</span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC230" class="line" lang="diff"><span class="p">@@ -121,8 +126,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC231" class="line" lang="diff"> public void testSamToCompactTrickCase12NoGenome() throws IOException {</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"> final String inputFile = "test-data/splicedsamhelper/tricky-spliced-12.sam";</span>
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<pre style="margin: 0;">+<span id="LC234" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC235" class="line" lang="diff"> final SamRecordParser recordParser = new SamRecordParser();</span>
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<pre style="margin: 0;">+<span id="LC236" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC237" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC238" 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="LC239" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC240" class="line" lang="diff"> for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {</span>
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<pre style="margin: 0;">+<span id="LC241" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC242" class="line" lang="diff"> final GobySamRecord gobySamRecord = recordParser.processRead(samRecord);</span>
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<pre style="margin: 0;">+<span id="LC243" class="line" lang="diff"><span class="p">@@ -146,7 +154,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC244" class="line" lang="diff"> public void testSamToCompactTrickCase13NoGenomeSoftClips() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC245" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC246" class="line" lang="diff"> final String inputFile = "test-data/splicedsamhelper/tricky-spliced-13.sam";</span>
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<pre style="margin: 0;">+<span id="LC247" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC248" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));</span></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;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC250" 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="LC251" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC252" class="line" lang="diff"> final SamRecordParser recordParser = new SamRecordParser();</span>
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<pre style="margin: 0;">+<span id="LC253" class="line" lang="diff"> for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {</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 class="p">@@ -179,8 +190,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC256" class="line" lang="diff"> public void testSamToCompactTrickCase13SoftClipsWithGenome() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC257" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC258" class="line" lang="diff"> final String inputFile = "test-data/splicedsamhelper/tricky-spliced-14.sam";</span>
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<pre style="margin: 0;">+<span id="LC259" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC260" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- parser.setValidationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC261" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC262" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC263" 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="LC264" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC265" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC266" class="line" lang="diff"> final SamRecordParser recordParser = new SamRecordParser();</span>
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<pre style="margin: 0;">+<span id="LC267" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC268" class="line" lang="diff"><span class="p">@@ -209,7 +222,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC269" class="line" lang="diff"> public void testSamToCompactTrickCase15NoGenomeThreeSplice() throws IOException {</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"> final String inputFile = "test-data/splicedsamhelper/tricky-spliced-15.sam";</span>
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272
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<pre style="margin: 0;">+<span id="LC272" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC273" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC274" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC275" 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="LC276" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC277" class="line" lang="diff"> final SamRecordParser recordParser = new SamRecordParser();</span>
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<pre style="margin: 0;">+<span id="LC278" class="line" lang="diff"> for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {</span>
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<pre style="margin: 0;">+<span id="LC279" class="line" lang="diff"> final GobySamRecord gobySamRecord = recordParser.processRead(samRecord);</span>
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<pre style="margin: 0;">+<span id="LC280" class="line" lang="diff"><span class="p">@@ -247,8 +263,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC281" class="line" lang="diff"> public void testSamToCompactTrickCase16() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC282" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC283" class="line" lang="diff"> final String inputFile = "test-data/splicedsamhelper/tricky-spliced-16.sam";</span>
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<pre style="margin: 0;">+<span id="LC284" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));</span></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;">- parser.setValidationStringency(ValidationStringency.SILENT);</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;">+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC287" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC288" 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="LC289" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC290" class="line" lang="diff"> final SamRecordParser recordParser = new SamRecordParser();</span>
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<pre style="margin: 0;">+<span id="LC291" class="line" lang="diff"> for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {</span>
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<pre style="margin: 0;">+<span id="LC292" class="line" lang="diff"> final GobySamRecord gobySamRecord = recordParser.processRead(samRecord);</span>
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<pre style="margin: 0;">+<span id="LC293" class="line" lang="diff"><span class="p">@@ -337,8 +355,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC294" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC295" class="line" lang="diff"> public void testSamToCompactTrickCase17() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC296" class="line" lang="diff"> final String inputFile = "test-data/splicedsamhelper/tricky-spliced-17.sam";</span>
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<pre style="margin: 0;">+<span id="LC297" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC298" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- parser.setValidationStringency(ValidationStringency.SILENT);</span></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;">+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC300" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC301" 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="LC302" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC303" class="line" lang="diff"> final SamRecordParser recordParser = new SamRecordParser();</span>
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<pre style="margin: 0;">+<span id="LC304" class="line" lang="diff"> for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {</span>
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<pre style="margin: 0;">+<span id="LC305" class="line" lang="diff"> final GobySamRecord gobySamRecord = recordParser.processRead(samRecord);</span>
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<pre style="margin: 0;">+<span id="LC306" class="line" lang="diff"><span class="p">@@ -422,8 +442,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC307" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC308" class="line" lang="diff"> public void testDelNonSplice1() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC309" class="line" lang="diff"> final String inputFile = "test-data/splicedsamhelper/del-nonsplice-1.sam";</span>
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<pre style="margin: 0;">+<span id="LC310" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC311" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- parser.setValidationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC312" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC313" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC314" 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="LC315" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC316" class="line" lang="diff"> final SamRecordParser recordParser = new SamRecordParser();</span>
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<pre style="margin: 0;">+<span id="LC317" class="line" lang="diff"> for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {</span>
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<pre style="margin: 0;">+<span id="LC318" class="line" lang="diff"> final GobySamRecord gobySamRecord = recordParser.processRead(samRecord);</span>
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<pre style="margin: 0;">+<span id="LC319" class="line" lang="diff"><span class="p">@@ -453,8 +475,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC320" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC321" class="line" lang="diff"> public void testLeftPadding1() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC322" class="line" lang="diff"> final String inputFile = "test-data/splicedsamhelper/leftpad-nosplice-1.sam";</span>
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323
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<pre style="margin: 0;">+<span id="LC323" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));</span></span>
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324
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<pre style="margin: 0;">+<span id="LC324" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- parser.setValidationStringency(ValidationStringency.SILENT);</span></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;">+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));</span></span>
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<pre style="margin: 0;">+<span id="LC326" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC327" 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="LC328" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC329" class="line" lang="diff"> final SamRecordParser recordParser = new SamRecordParser();</span>
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<pre style="margin: 0;">+<span id="LC330" class="line" lang="diff"> for (final SAMRecord samRecord : new SAMRecordIterable(parser.iterator())) {</span>
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<pre style="margin: 0;">+<span id="LC331" class="line" lang="diff"> final GobySamRecord gobySamRecord = recordParser.processRead(samRecord);</span>
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<pre style="margin: 0;">+<span id="LC332" class="line" lang="diff"><span class="p">@@ -491,8 +515,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC333" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC334" class="line" lang="diff"> public void testSeqVarReads() throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC335" class="line" lang="diff"> final String inputFile = "test-data/seq-var-test/seq-var-reads-gsnap.sam";</span>
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<pre style="margin: 0;">+<span id="LC336" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final SAMFileReader parser = new SAMFileReader(new FileInputStream(inputFile));</span></span>
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337
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<pre style="margin: 0;">+<span id="LC337" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- parser.setValidationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC338" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamInputResource sir = SamInputResource.of(new FileInputStream(inputFile));</span></span>
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339
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<pre style="margin: 0;">+<span id="LC339" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReaderFactory srf = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);</span></span>
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<pre style="margin: 0;">+<span id="LC340" 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="LC341" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final SamReader parser = srf.open(sir);</span></span>
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<pre style="margin: 0;">+<span id="LC342" class="line" lang="diff"> final SamRecordParser recordParser = new SamRecordParser();</span>
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<pre style="margin: 0;">+<span id="LC343" class="line" lang="diff"> final PositionToBasesMap<PerQueryAlignmentData> seqvarDataMap = TestIteratedSortedAlignment2.readSeqVarFile(</span>
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<pre style="margin: 0;">+<span id="LC344" class="line" lang="diff"> "test-data/seq-var-test/seq-var-reads-gsnap.seqvar");</span></pre>
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<li id="cf3fc76fed161bccf82d0e694add0230b157ccc7">
<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#cf3fc76fed161bccf82d0e694add0230b157ccc7"><strong>debian/patches/using_jbzip2.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-distribution/src/main/java/org/campagnelab/goby/compression/BZip2ChunkCodec.java</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-distribution/src/main/java/org/campagnelab/goby/compression/BZip2ChunkCodec.java</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">@@ -19,8 +19,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> package org.campagnelab.goby.compression;</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"> import com.google.protobuf.Message;</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.apache.tools.bzip2.CBZip2InputStream;</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import org.apache.tools.bzip2.CBZip2OutputStream;</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.itadaki.bzip2.BZip2InputStream;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+import org.itadaki.bzip2.BZip2OutputStream;</span></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"> import java.io.*;</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="p">@@ -76,7 +76,7 @@</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"> byteBuffer.write(magicSignature);</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final OutputStream bZip2OutputStream = new CBZip2OutputStream(byteBuffer);</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final OutputStream bZip2OutputStream = new BZip2OutputStream(byteBuffer);</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> readCollection.writeTo(bZip2OutputStream);</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> bZip2OutputStream.flush();</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> bZip2OutputStream.close();</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -93,7 +93,7 @@</span></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>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> // remove the magic numbers:</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final CBZip2InputStream uncompressStream = new CBZip2InputStream(new ByteArrayInputStream(bytes, 3, bytes.length));</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 BZip2InputStream uncompressStream = new BZip2InputStream(new ByteArrayInputStream(bytes, 3, bytes.length), false);</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"> try {</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"> return parser.parse(uncompressStream);</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> } finally {</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/goby-io/pom.xml</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/goby-io/pom.xml</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="p">@@ -451,6 +451,14 @@</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> <version>debian</version></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> </dependency></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> </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;">+ <dependency></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;">+ <groupId>org.itadaki</groupId></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;">+ <artifactId>bzip2</artifactId></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;">+ <version>0.9.1</version></span></span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ <scope>system</scope></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;">+ <systemPath>/usr/share/java/jbzip2-0.9.1.jar</systemPath></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;">+ </dependency></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;">+</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> </dependencies></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> </project></span></pre>
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<a href="https://salsa.debian.org/med-team/libgoby-java/-/compare/e007855ad41bb8220531536dc66c3e679a17df41...1e72a3f187f726b1f77b1b27323c42aa69ca70cb#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</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">@@ -16,3 +16,15 @@</td>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"># dh_auto_configure</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"># ln -s ../debian/buildsupport/build.xml buildsupport/build.xml</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"># ln -s ../debian/buildsupport/gitant buildsupport/gitant</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">override_dh_auto_clean:</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> dh_auto_clean</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> $(RM) goby-distribution/test-data</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext"> # Create a symlink to the directory with test data for tests run from the</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext"> # goby-distribution directory.</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> ln -s ../test-data goby-distribution/test-data</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> dh_auto_test</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">endif</span></pre>
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