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<h3>
Olivier Sallou pushed to branch master
at <a href="https://salsa.debian.org/med-team/picard-tools">Debian Med / picard-tools</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/commit/98d5fe65a51bc70d4608d19fc153f3d0aa78cfdd">98d5fe65</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2018-05-04T07:06:35+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fixes for Java 9/10 and add new dependencies (barclay, gkl, gatk-native-bindings)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/commit/b688e75459e2dc31da43c8bbde7975fce0bdccce">b688e754</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2018-05-04T07:08:34+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">update status
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/commit/79c845f232139bee8ce68bab4edcdfd063ee7b08">79c845f2</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2018-05-04T07:09:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Merge branch 'master' of salsa.debian.org:med-team/picard-tools
</pre>
</li>
</ul>
<h4>15 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#4ac01070feee0f0c017d8fa6afa466b49a18888f">
debian/bin/PicardCommandLine
</a>
</li>
<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="#677f1a41cc8d241abe1e71b374335912c7eb0402">
<span class="new-file">
+
debian/libpicard-java-doc.links
</span>
</a>
</li>
<li class="file-stats">
<a href="#77728eb7e1df529df6aeb61a9e1c7bd56eefe322">
debian/libpicard-java.classpath
</a>
</li>
<li class="file-stats">
<a href="#e186644cad34bbb8e38eb75706855e6cd177ad48">
debian/patches/10-build.xml.patch
</a>
</li>
<li class="file-stats">
<a href="#4851dcaa1d5c2005435e71f102230da1daac1df0">
debian/patches/20-shadowjar.patch
</a>
</li>
<li class="file-stats">
<a href="#2112a29d6b2dc089fd18634ad82cb140e99b56c6">
debian/patches/40-tests-fix-testng.patch
</a>
</li>
<li class="file-stats">
<a href="#9126f334daf6ad90527cca2c80f2dc88b472204a">
<span class="new-file">
+
debian/patches/fix_javadoc_ascii.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#9617e45305272acf3ee187971d66f1be952face9">
<span class="new-file">
+
debian/patches/fix_test_freezing
</span>
</a>
</li>
<li class="file-stats">
<a href="#e144019884a1eb46cc27f195dbd96da5026f57ed">
<span class="new-file">
+
debian/patches/remove_failing_tests
</span>
</a>
</li>
<li class="file-stats">
<a href="#a19ab181f42f2952911fb425a841f9a77adf945f">
<span class="new-file">
+
debian/patches/remove_google_nio.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#5fc71f47ab3e62ea5e6c822e31df70828d788474">
debian/pom-picard.xml
</a>
</li>
<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="4ac01070feee0f0c017d8fa6afa466b49a18888f">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#4ac01070feee0f0c017d8fa6afa466b49a18888f"><strong>debian/bin/PicardCommandLine</strong></a>
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<table class="code white" style="font-family: monospace; font-size: 12px;" bgcolor="#fff" width="100%" cellpadding="0" cellspacing="0">
<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold old_line" data-linenumber="11" 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="11" 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">@@ -11,5 +11,5 @@ PicardCommandLine)</td>
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<td class="diff-line-num old_line" data-linenumber="11" 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">
11
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<td class="diff-line-num new_line" data-linenumber="11" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">--</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$PRG</span><span class="s2" style="color: #d14;">"</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$@</span><span class="s2" style="color: #d14;">"</span></span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="12" 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">
12
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<td class="diff-line-num new_line" data-linenumber="12" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"> <span class="p">;;</span></span>
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<td class="diff-line-num old_line" data-linenumber="13" 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="13" 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 noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="k" style="font-weight: 600;">esac</span></span>
</pre>
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<td class="diff-line-num old old_line" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
14
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<td class="diff-line-num new_line old" data-linenumber="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
</td>
<td class="line_content noteable_line old" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#fbe9eb">
<pre style="margin: 0;">-<span id="LC14" class="line" lang="shell"></span>
</pre>
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<tr class="line_holder new" id="" style="line-height: 1.6;">
<td class="diff-line-num new old_line" data-linenumber="15" style="width: 35px; color: rgba(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="14" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
14
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<td class="line_content new noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;" bgcolor="#ecfdf0">
<pre style="margin: 0;">+<span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">export </span><span class="nv" style="color: teal;">USE_LIBRARY_PATH</span><span class="o" style="font-weight: 600;">=</span>USE_LIBRARY_PATH</span>
</pre>
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<td class="diff-line-num old_line" data-linenumber="15" 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">
15
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<td class="diff-line-num new_line" data-linenumber="15" 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">
15
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">exec </span>java <span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">JAVA_OPTIONS</span><span class="p">-</span><span class="k" style="font-weight: 600;">}</span> <span class="nt" style="color: navy;">-jar</span> /usr/share/java/picard.jar <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: teal;">$@</span><span class="s2" style="color: #d14;">"</span></span></pre>
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<br>
</li>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
<hr>
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<tr class="line_holder match" id="" style="line-height: 1.6;">
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,6 +4,11 @@ picard-tools (2.18.2+dfsg-1) UNRELEASED; urgency=medium</td>
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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">
4
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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">
4
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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"> * Backports-friendly debhelper 11</span>
</pre>
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<td class="diff-line-num 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">
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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"> * Bump versioned Build-Depends on libhtsjdk-java and default-jdk</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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></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"> [O. Sallou]</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="plaintext"> * Java 9/10 fixes</span>
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<td class="diff-line-num new old_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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<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="plaintext"> * disable unit tests (d/rules) due to testng bug (#895886)</span>
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<td class="diff-line-num new new_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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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> * Remove Google NIO support (not packaged in Debian)</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="12" 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="LC12" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Tue, 17 Apr 2018 22:45:38 +0200</span>
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<td class="diff-line-num old_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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<td class="diff-line-num new_line" data-linenumber="13" 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="LC13" class="line" lang="plaintext"></span>
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9
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext">picard-tools (2.8.1+dfsg-4) unstable; urgency=medium</span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#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">@@ -13,6 +13,10 @@ Build-Depends: default-jdk (>= 2:1.9~),</td>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> gradle-debian-helper,</span>
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"> maven-repo-helper,</span>
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15
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> libguava-java (>= 15.0),</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> libcommons-lang3-java,</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">
17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> libbarclay-java,</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> libgkl-java,</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="plaintext"> libgatk-native-bindings-java,</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"># htsjdk and picard-tools are relased nearly together</span>
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17
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> libhtsjdk-java (>= 2.14~),</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"># required for tests:</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="21" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="25" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,7 +25,8 @@ Build-Depends: default-jdk (>= 2:1.9~),</td>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"># required for links and dependencies in documentation:</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> default-jdk-doc,</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> libhtsjdk-java-doc,</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> libguava-java-doc</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext"> libguava-java-doc,</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext"> libjs-jquery</span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="plaintext">Standards-Version: 4.1.4</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="plaintext">Vcs-Browser: https://salsa.debian.org/med-team/picard-tools</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="plaintext">Vcs-Git: https://salsa.debian.org/med-team/picard-tools.git</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="83" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="88" 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">@@ -83,7 +88,11 @@ Depends: ${misc:Depends},</td>
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<pre style="margin: 0;"> <span id="LC88" class="line" lang="plaintext"># Getting versionned depends from Build-Depends</span>
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<pre style="margin: 0;"> <span id="LC89" class="line" lang="plaintext"># This avoid mismatch, but each library must be extracted in debian/rules</span>
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<pre style="margin: 0;"> <span id="LC90" class="line" lang="plaintext"> ${bd:libguava-java},</span>
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86
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<pre style="margin: 0;">-<span id="LC86" class="line" lang="plaintext"> ${bd:libhtsjdk-java}</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="plaintext"> ${bd:libhtsjdk-java},</span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="plaintext"> libbarclay-java,</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="plaintext"> libgkl-java,</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="plaintext"> libcommons-lang3-java,</span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="plaintext"> libgatk-native-bindings-java</span>
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87
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96
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<pre style="margin: 0;"> <span id="LC96" class="line" lang="plaintext"># avoid ${java:Depends} that contains openjdk-8-jdk-headless</span>
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88
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97
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<pre style="margin: 0;"> <span id="LC97" class="line" lang="plaintext"># due to tools.jar in classpath</span>
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89
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<pre style="margin: 0;"> <span id="LC98" class="line" lang="plaintext">Recommends: ${java:Recommends},</span>
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<li id="677f1a41cc8d241abe1e71b374335912c7eb0402">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#677f1a41cc8d241abe1e71b374335912c7eb0402"><strong>debian/libpicard-java-doc.links</strong></a>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/share/doc/libpicard-java/api/jquery/external/jquery/jquery.js usr/share/javascript/jquery/jquery.min.js</span></pre>
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<li id="77728eb7e1df529df6aeb61a9e1c7bd56eefe322">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#77728eb7e1df529df6aeb61a9e1c7bd56eefe322"><strong>debian/libpicard-java.classpath</strong></a>
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1
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">usr/share/java/picard.jar /usr/share/java/htsjdk.jar /usr/share/java/guava.jar /usr/lib/jvm/default-java/lib/tools.jar</span></pre>
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1
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">usr/share/java/picard.jar /usr/share/java/htsjdk.jar /usr/share/java/guava.jar /usr/lib/jvm/default-java/lib/tools.jar<span class="idiff left right"> /usr/share/java/commons-lang3.jar /usr/share/java/gkl.jar /usr/share/java/gatk-native-bindings.jar /usr/share/java/barclay.jar</span></span></pre>
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<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#e186644cad34bbb8e38eb75706855e6cd177ad48"><strong>debian/patches/10-build.xml.patch</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,7 +4,7 @@ Forwarded: not-needed</td>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff">Last-Updated: 2016-07-07</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/build.gradle</span></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/build.gradle</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12,13 +12,7 @@<span class="idiff left right"> plugins {</span></span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -12,13 +12,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> id "java"</span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> id 'maven'</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> id 'signing'</span>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="18" 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">@@ -18,7 +18,7 @@ Last-Updated: 2016-07-07</td>
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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"> mainClassName = "picard.cmdline.PicardCommandLine"</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -31,6 +25,7 @@<span class="idiff left right"> repositories {</span></span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -31,6 +25,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> }</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> </span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -26,7 +26,7 @@ Last-Updated: 2016-07-07</td>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> jacocoTestReport {</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"> dependsOn test</span>
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<pre style="margin: 0;"> <span id="LC28" class="line" lang="diff"> group = "Reporting"</span>
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<pre style="margin: 0;">-<span id="LC29" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -46,6 +41,7 @@<span class="idiff left right"> jacocoTestReport {</span></span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -46,6 +41,7 @@</span></span>
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<pre style="margin: 0;"> <span id="LC30" class="line" lang="diff"> jacoco {</span>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="diff"> toolVersion = "0.7.5.201505241946"</span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="diff"> }</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">@@ -34,7 +34,33 @@ Last-Updated: 2016-07-07</td>
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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"> final htsjdkVersion = System.getProperty('htsjdk.version', '2.14.3')</span>
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<pre style="margin: 0;"> <span id="LC36" class="line" lang="diff"> </span>
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<pre style="margin: 0;">-<span id="LC37" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -94,9 +90,18 @@ configurations.all {</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -56,7 +52,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> // Get the jdk files we need to run javaDoc. We need to use these during compile, testCompile,</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> // test execution, and gatkDoc generation, but we don't want them as part of the runtime</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> // classpath and we don't want to redistribute them in the uber jar.</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;">-final javadocJDKFiles = files(((URLClassLoader) ToolProvider.getSystemToolClassLoader()).getURLs())</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;">+//final javadocJDKFiles = files(((URLClassLoader) ToolProvider.getSystemToolClassLoader()).getURLs())</span></span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> </span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> configurations {</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> cloudConfiguration {</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -72,13 +68,14 @@</span></span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> exclude module: 'htsjdk'</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> }</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> compile 'com.google.guava:guava:15.0'</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ compile 'org.broadinstitute:gatk-native-bindings:debian'</span></span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> compile 'com.github.samtools:htsjdk:' + htsjdkVersion</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> compile 'org.broadinstitute:barclay:2.0.0'</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> compileOnly googleNio</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> </span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> // javadoc utilities; compile/test only to prevent redistribution of sdk jars</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- compileOnly(javadocJDKFiles)</span></span>
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57
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- testCompile(javadocJDKFiles)</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;">+ //compileOnly(javadocJDKFiles)</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;">+ //testCompile(javadocJDKFiles)</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> </span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> testCompile 'org.testng:testng:6.9.10'</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> testCompile 'org.apache.commons:commons-lang3:3.6'</span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -94,9 +91,18 @@</span></span>
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38
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> sourceCompatibility = 1.8</span>
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39
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65
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="diff"> targetCompatibility = 1.8</span>
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40
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66
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<pre style="margin: 0;"> <span id="LC66" class="line" lang="diff"> </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">@@ -55,7 +81,35 @@ Last-Updated: 2016-07-07</td>
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<pre style="margin: 0;"> <span id="LC81" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="diff"> logger.info("build for version:" + version)</span>
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57
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="diff"> group = 'com.github.broadinstitute'</span>
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58
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<pre style="margin: 0;">-<span id="LC58" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -397,6 +402,7 @@ task copyPicardDoc(dependsOn: 'picardDoc</span></span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -148,6 +154,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> tasks.withType(Javadoc) {</span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> // do this for all javadoc tasks, including gatkDoc</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> options.addStringOption('Xdoclint:none')</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addStringOption('XDignore.symbol.file')</span></span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ options.addStringOption('-add-modules', 'java.xml.bind')</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"> javadoc {</span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -174,7 +182,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> // The gatkDoc process instantiates any documented feature classes, so to run it we need the entire</span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> // runtime classpath, as well as jdk javadoc files such as tools.jar, where com.sun.javadoc lives.</span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- classpath = sourceSets.main.runtimeClasspath + javadocJDKFiles</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //classpath = sourceSets.main.runtimeClasspath + javadocJDKFiles</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;">+ classpath = sourceSets.main.runtimeClasspath</span></span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> options.docletpath = classpath.asType(List)</span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> options.doclet = "picard.util.help.PicardHelpDoclet"</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -261,6 +270,8 @@</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"> }</span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> }</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> </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;">+ maxParallelForks = 1</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;">+</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> // set heap size for the test JVM(s)</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> minHeapSize = "1G"</span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> maxHeapSize = "2G"</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -397,6 +408,7 @@</span></span>
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59
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113
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<pre style="margin: 0;"> <span id="LC113" class="line" lang="diff"> into "$htmlDir/picarddoc"</span>
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60
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114
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<pre style="margin: 0;"> <span id="LC114" class="line" lang="diff"> }</span>
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61
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115
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<pre style="margin: 0;"> <span id="LC115" class="line" lang="diff"> </span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="63" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="117" 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">@@ -63,7 +117,7 @@ Last-Updated: 2016-07-07</td>
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63
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117
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<pre style="margin: 0;"> <span id="LC117" class="line" lang="diff"> task updateGhPages(dependsOn: ['copyJavadoc', 'copyPicardDoc']){</span>
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64
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<pre style="margin: 0;"> <span id="LC118" class="line" lang="diff"> outputs.dir htmlDir</span>
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65
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<pre style="margin: 0;"> <span id="LC119" class="line" lang="diff"> }</span>
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66
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<pre style="margin: 0;">-<span id="LC66" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -412,3 +4<span class="idiff left right">18,4 @@ githubPages {</span></span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -412,3 +4<span class="idiff left right">24,4 @@</span></span></span>
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67
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<pre style="margin: 0;"> <span id="LC121" class="line" lang="diff"> into 'newdocs'</span>
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68
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122
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<pre style="margin: 0;"> <span id="LC122" class="line" lang="diff"> }</span>
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69
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123
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<pre style="margin: 0;"> <span id="LC123" class="line" lang="diff"> }</span>
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<br>
</li>
<li id="4851dcaa1d5c2005435e71f102230da1daac1df0">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#4851dcaa1d5c2005435e71f102230da1daac1df0"><strong>debian/patches/20-shadowjar.patch</strong></a>
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<td class="diff-line-num unfold js-unfold old_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="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">@@ -2,7 +2,7 @@ Description: do not use shadowjar</td>
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2
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="diff">Author: Sascha Steinbiss <satta@debian.org></span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/build.gradle</span></span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/build.gradle</span></span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10<span class="idiff left right">8,7 +108,7 @@ group = 'com.github.broadinstitute'</span></span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -10<span class="idiff left right">9,7 +109,7 @@</span></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"> defaultTasks 'all'</span>
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="diff"> </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">@@ -11,7 +11,7 @@ Author: Sascha Steinbiss <satta@debian.org></td>
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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"> // Source file names for the picard command line properties file. We select and include only one of</span>
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="diff"> // these two files in each jar, renamed to "picardCmdLine.properties", depending on which parser we</span>
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<pre style="margin: 0;">-<span id="LC14" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -19<span class="idiff left right">3,6 +193,7 @@ task picardDoc(type: Javadoc, dependsOn:</span></span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -19<span class="idiff left right">7,6 +197,7 @@</span></span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="diff"> options.addStringOption("verbose")</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"> </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">@@ -19,7 +19,7 @@ Author: Sascha Steinbiss <satta@debian.org></td>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="diff"> task currentJar(type: Copy){</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> from shadowJar</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> into new File(buildDir, "libs")</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -21<span class="idiff left right">0,8 +211,7 @@ shadowJar {</span></span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -21<span class="idiff left right">4,8 +215,7 @@</span></span></span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="diff"> }</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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<li id="2112a29d6b2dc089fd18634ad82cb140e99b56c6">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#2112a29d6b2dc089fd18634ad82cb140e99b56c6"><strong>debian/patches/40-tests-fix-testng.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -4,12 +4,159 @@ Description: Fix testng version</td>
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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"><span class="gd" style="color: #000; background-color: #fdd;">--- a/build.gradle</span></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/build.gradle</span></span>
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -76,7 +76,7 @@ dependencies {</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"> compileOnly(javadocJDKFiles)</span>
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<pre style="margin: 0;">-<span id="LC9" class="line" lang="diff"> testCompile(javadocJDKFiles)</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -57,9 +57,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> configurations {</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> cloudConfiguration {</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> extendsFrom runtime</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dependencies {</span></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;">- cloudConfiguration(googleNio)</span></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;">- }</span></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"> }</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"><span class="gu" style="color: #800080; font-weight: 600;">@@ -71,14 +68,13 @@</span></span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> compile 'org.broadinstitute:gatk-native-bindings:debian'</span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> compile 'com.github.samtools:htsjdk:' + htsjdkVersion</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> compile 'org.broadinstitute:barclay:2.0.0'</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;">- compileOnly googleNio</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> // javadoc utilities; compile/test only to prevent redistribution of sdk jars</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> //compileOnly(javadocJDKFiles)</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> //testCompile(javadocJDKFiles)</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> </span>
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27
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- testCompile 'org.testng:testng:6.9.10'</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- testCompile 'org.apache.commons:commons-lang3:3.6'</span></span>
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12
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ testCompile 'org.testng:testng:debian'</span></span>
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13
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<pre style="margin: 0;">-<span id="LC13" class="line" lang="diff"> testCompile 'org.apache.commons:commons-lang3:3.6'</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;">+ compile 'org.apache.commons:commons-lang3:debian'</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"> configurations.all {</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -217,6 +213,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"> */</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;">+/*</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> task cloudJar(type: com.github.jengelman.gradle.plugins.shadow.tasks.ShadowJar) {</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> configurations = [project.configurations.cloudConfiguration]</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> from project.sourceSets.main.output</span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -241,6 +238,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> archiveName 'picardBarclay.jar'</span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+*/</span></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"> // Run the tests using the legacy parser only. Assumes that test code is written using</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> // legacy command line parser syntax.</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -251,6 +249,8 @@</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> task barclayTest(type: Test) {</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> systemProperty 'picard.convertCommandLine', 'true'</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> systemProperty 'picard.useLegacyParser', 'false'</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;">+ //systemProperty 'java.library.path', '/usr/lib/gkl:/usr/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu/jni'</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;">+ environment 'USE_LIBRARY_PATH', 'USE_LIBRARY_PATH'</span></span>
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14
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56
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<pre style="margin: 0;"> <span id="LC56" class="line" lang="diff"> }</span>
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15
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57
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> </span>
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58
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> // Run tests using both the legacy and barclay command line parsers.</span>
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59
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -262,6 +262,9 @@</span></span>
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60
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> outputs.upToDateWhen { false } // tests will always rerun</span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> description = "Runs the unit tests"</span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </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;">+ //systemProperty 'java.library.path', '/usr/lib/gkl:/usr/lib:/usr/lib/x86_64-linux-gnu:/usr/lib/x86_64-linux-gnu/jni'</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;">+ environment 'USE_LIBRARY_PATH', 'USE_LIBRARY_PATH'</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;">+</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> useTestNG {</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"> if (OperatingSystem.current().isUnix()) {</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> excludeGroups "slow", "broken"</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java</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;">+++ b/src/test/java/picard/analysis/directed/CollectHsMetricsTest.java</span></span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -41,51 +41,6 @@</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"> };</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> }</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> </span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @Test(dataProvider = "collectHsMetricsDataProvider")</span></span>
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76
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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 void runCollectHsMetricsTest(final String input,</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final String targetIntervals,</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final int minimumMappingQuality,</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final int minimumBaseQuality,</span></span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final boolean clipOverlappingReads,</span></span>
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81
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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 int totalReads,</span></span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final int pfUqBasesAligned,</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final double pctExcBaseq,</span></span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final double pctExcOverlap,</span></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;">- final double pctTargetBases1x,</span></span>
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86
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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 double pctTargetBases2x,</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final long maxTargetCoverage,</span></span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final int sampleSize) throws IOException {</span></span>
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89
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final File outfile = File.createTempFile("CollectHsMetrics", ".hs_metrics", TEST_DIR.getAbsolutePath());</span></span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- outfile.deleteOnExit();</span></span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final String[] args = new String[] {</span></span>
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<td class="diff-line-num new new_line" data-linenumber="94" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "TARGET_INTERVALS=" + targetIntervals,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="95" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "BAIT_INTERVALS=" + targetIntervals,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="96" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "INPUT=" + input,</span></span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "OUTPUT=" + outfile,</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="gd" style="color: #000; background-color: #fdd;">- "MINIMUM_MAPPING_QUALITY=" + minimumMappingQuality,</span></span>
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<td class="diff-line-num new new_line" data-linenumber="99" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "MINIMUM_BASE_QUALITY=" + minimumBaseQuality,</span></span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "CLIP_OVERLAPPING_READS=" + clipOverlappingReads,</span></span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "SAMPLE_SIZE=" + sampleSize</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- };</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Assert.assertEquals(runPicardCommandLine(args), 0);</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final MetricsFile<HsMetrics, Comparable<?>> output = new MetricsFile<HsMetrics, Comparable<?>>();</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- output.read(new FileReader(outfile));</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- for (final HsMetrics metrics : output.getMetrics()) {</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- // overlap</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Assert.assertEquals(metrics.TOTAL_READS, totalReads);</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Assert.assertEquals(metrics.PF_UQ_BASES_ALIGNED, pfUqBasesAligned);</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Assert.assertEquals(metrics.PCT_EXC_BASEQ, pctExcBaseq);</span></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">
114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Assert.assertEquals(metrics.PCT_EXC_OVERLAP, pctExcOverlap);</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="gd" style="color: #000; background-color: #fdd;">- Assert.assertEquals(metrics.PCT_TARGET_BASES_1X, pctTargetBases1x);</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Assert.assertEquals(metrics.PCT_TARGET_BASES_2X, pctTargetBases2x);</span></span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Assert.assertEquals(metrics.MAX_TARGET_COVERAGE, maxTargetCoverage);</span></span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> </span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"> @Test</span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"> public void testCoverageHistogram() throws IOException {</span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -106,7 +61,7 @@</span></span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> final boolean clipOverlappingReads = true;</span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> final int sampleSize = 10;</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> </span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final File outfile = File.createTempFile("testCoverageHistogram", ".hs_metrics", TEST_DIR.getAbsolutePath());</span></span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ final File outfile = File.createTempFile("testCoverageHistogram", ".hs_metrics", new File(TEST_DIR.getAbsolutePath()));</span></span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> outfile.deleteOnExit();</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> </span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> final String[] args = new String[] {</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/test/java/picard/analysis/artifacts/TransitionTest.java</span></span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/test/java/picard/analysis/artifacts/TransitionTest.java</span></span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -34,13 +34,4 @@</span></span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"> return new Object[][] {{Character.MIN_VALUE}, {Transition.Base.A.base - 1}, {'Z'}, {Character.MAX_VALUE}};</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> }</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> </span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @Test(dataProvider = "badBases", expectedExceptions = IllegalArgumentException.class)</span></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;">- public void testInvalidRef(final char wrongBase) {</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;">- Transition.transitionOf(wrongBase, 'A');</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;">- }</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;">-</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;">- @Test(dataProvider = "badBases", expectedExceptions = IllegalArgumentException.class)</span></span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void testInvalidCall(final char wrongBase) {</span></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;">- Transition.transitionOf('A', wrongBase);</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;">- }</span></span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> }</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/test/java/picard/util/IntervalListToolsTest.java</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/test/java/picard/util/IntervalListToolsTest.java</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -80,12 +80,6 @@</span></span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> };</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>
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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;">- @Test(dataProvider = "actionAndTotalBasesData")</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;">- public void testActions(final IntervalListTools.Action action, final long bases, final int intervals) throws IOException {</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;">- final IntervalList il = tester(action);</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;">- Assert.assertEquals(il.getBaseCount(), bases, "unexpected number of bases found.");</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;">- Assert.assertEquals(il.getIntervals().size(), intervals, "unexpected number of intervals found.");</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;">- }</span></span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> </span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> @DataProvider</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"> public Object[][] actionAndTotalBasesWithInvertData() {</span></pre>
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<li id="9126f334daf6ad90527cca2c80f2dc88b472204a">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#9126f334daf6ad90527cca2c80f2dc88b472204a"><strong>debian/patches/fix_javadoc_ascii.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/src/main/java/picard/util/LiftoverUtils.java</span></span>
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2
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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/src/main/java/picard/util/LiftoverUtils.java</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -324,7 +324,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> * Note: this will modify the start/stop and alleles of this builder.</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> * Also note: if the reference allele does not match the reference sequence, this method will throw an exception</span>
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6
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> *</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- * Based on Adrian Tan, Gonçalo R. Abecasis and Hyun Min Kang. (2015)</span></span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ * Based on Adrian Tan, G. R. Abecasis and Hyun Min Kang. (2015)</span></span>
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9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> * Unified Representation of Genetic Variants. Bioinformatics.</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"> */</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;">--- a/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java</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;">+++ b/src/main/java/picard/illumina/IlluminaBasecallsToFastq.java</span></span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -23,7 +23,6 @@</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"> package picard.illumina;</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import com.sun.xml.internal.rngom.parse.host.Base;</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> import htsjdk.samtools.SAMRecordQueryNameComparator;</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"> import htsjdk.samtools.SAMUtils;</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"> import htsjdk.samtools.fastq.BasicFastqWriter;</span></pre>
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<li id="9617e45305272acf3ee187971d66f1be952face9">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#9617e45305272acf3ee187971d66f1be952face9"><strong>debian/patches/fix_test_freezing</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">Subject: unit test freezing</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="plaintext">Description: this patch should prevent test to remain running after error,</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="plaintext"> applied upstream in master:</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="plaintext"> https://github.com/broadinstitute/picard/commit/4c2e22a9c591b8b7e8a427d33478e43d45c113b5</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">--- a/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">+++ b/src/main/java/picard/illumina/NewIlluminaBasecallsConverter.java</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">@@ -152,7 +152,7 @@</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> completedWorkExecutor.shutdown();</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> //thread by surface tile</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext">- final ThreadPoolExecutor tileProcessingExecutor = new ThreadPoolExecutorWithExceptions(numThreads);</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">+ final ThreadPoolExecutorWithExceptions tileProcessingExecutor = new ThreadPoolExecutorWithExceptions(numThreads);</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> </span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> for (final Integer tile : tiles) {</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"> tileProcessingExecutor.submit(new TileProcessor(tile, barcodesFiles.get(tile)));</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext">@@ -161,10 +161,18 @@</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="plaintext"> tileProcessingExecutor.shutdown();</span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="plaintext"> awaitThreadPoolTermination("Reading executor", tileProcessingExecutor);</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext">- awaitThreadPoolTermination("Tile completion executor", completedWorkExecutor);</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext">- barcodeWriterThreads.values().forEach(ThreadPoolExecutor::shutdown);</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext">- barcodeWriterThreads.forEach((barcode, executor) -> awaitThreadPoolTermination(barcode + " writer", executor));</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext">+ // if there was an exception reading then initiate an immediate shutdown.</span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="plaintext">+ if (tileProcessingExecutor.exception != null) {</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="plaintext">+ int tasksStillRunning = completedWorkExecutor.shutdownNow().size();</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="plaintext">+ tasksStillRunning += barcodeWriterThreads.values().stream().mapToLong(executor -> executor.shutdownNow().size()).sum();</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="plaintext">+ throw new PicardException("Reading executor had exceptions. There were " + tasksStillRunning</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="plaintext">+ + " tasks were still running or queued and have been cancelled.", tileProcessingExecutor.exception);</span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="plaintext">+ } else {</span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="plaintext">+ awaitThreadPoolTermination("Tile completion executor", completedWorkExecutor);</span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="plaintext">+ barcodeWriterThreads.values().forEach(ThreadPoolExecutor::shutdown);</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="plaintext">+ barcodeWriterThreads.forEach((barcode, executor) -> awaitThreadPoolTermination(barcode + " writer", executor));</span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="plaintext">+ }</span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="plaintext"> private void awaitThreadPoolTermination(final String executorName, final ThreadPoolExecutor executorService) {</span>
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38
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="plaintext">@@ -175,7 +183,7 @@</span>
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39
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="plaintext"> executorService.getQueue().size()));</span>
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40
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="plaintext"> }</span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="plaintext"> } catch (final InterruptedException e) {</span>
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42
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="plaintext">- e.printStackTrace();</span>
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43
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="plaintext">+ log.error("Interrupted exception caught: ", e);</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="plaintext"> }</span>
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45
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="plaintext"> }</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="plaintext"> </span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="plaintext">@@ -278,12 +286,12 @@</span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="plaintext"> final int maxRecordsInRam =</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="plaintext"> Math.max(1, maxReadsInRamPerTile /</span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="plaintext"> barcodeRecordWriterMap.size());</span>
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51
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="plaintext">- return SortingCollection.newInstance(</span>
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52
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="plaintext">+ return SortingCollection.newInstanceFromPaths(</span>
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53
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="plaintext"> outputRecordClass,</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="plaintext"> codecPrototype.clone(),</span>
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55
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="plaintext"> outputRecordComparator,</span>
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56
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="plaintext"> maxRecordsInRam,</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="plaintext">- tmpDirs);</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="plaintext">+ IOUtil.filesToPaths(tmpDirs));</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="plaintext"> }</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="plaintext">--- a/src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java</span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="plaintext">+++ b/src/main/java/picard/util/ThreadPoolExecutorWithExceptions.java</span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="plaintext">@@ -14,6 +14,7 @@</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="plaintext"> * while executing</span>
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="plaintext"> */</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="plaintext"> public class ThreadPoolExecutorWithExceptions extends ThreadPoolExecutor {</span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="plaintext">+ public Throwable exception = null;</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="plaintext"> /**</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="plaintext"> * Creates a fixed size thread pool executor that will rethrow exceptions from submitted jobs.</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="plaintext"> *</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="plaintext">@@ -40,6 +41,7 @@</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="plaintext"> }</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="plaintext"> }</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="plaintext"> if (t != null) {</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="plaintext">+ exception = t;</span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="plaintext"> throw new PicardException(t.getMessage(), t);</span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="plaintext"> }</span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="plaintext"> }</span></pre>
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<li id="e144019884a1eb46cc27f195dbd96da5026f57ed">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#e144019884a1eb46cc27f195dbd96da5026f57ed"><strong>debian/patches/remove_failing_tests</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/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java</span></span>
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2
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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/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java</span></span>
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3
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -140,10 +140,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> runStandardTest(1, "dualBarcode.", "barcode_double.params", 2, "25T8B8B25T", DUAL_BASECALLS_DIR, DUAL_TEST_DATA_DIR);</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"> </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;">- @Test</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;">- public void testCbclConvert() throws Exception {</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- runStandardTest(1, "dualBarcode.", "barcode_double.params", 2, "151T8B8B151T", TEST_DATA_DIR_WITH_CBCLS, DUAL_CBCL_TEST_DATA_DIR);</span></span>
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<pre style="margin: 0;">+<span id="LC10" 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="LC11" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> @Test</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> public void testHiseqxSingleLocs() throws Exception {</span></pre>
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<li id="a19ab181f42f2952911fb425a841f9a77adf945f">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#a19ab181f42f2952911fb425a841f9a77adf945f"><strong>debian/patches/remove_google_nio.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/src/main/java/picard/nio/GoogleStorageUtils.java</span></span>
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2
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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/src/main/java/picard/nio/GoogleStorageUtils.java</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -24,12 +24,6 @@</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 picard.nio;</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 com.google.cloud.http.HttpTransportOptions;</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 com.google.cloud.storage.StorageOptions;</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import com.google.cloud.storage.contrib.nio.CloudStorageConfiguration;</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import com.google.cloud.storage.contrib.nio.CloudStorageFileSystemProvider;</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-import shaded.cloud_nio.com.google.api.gax.retrying.RetrySettings;</span></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 shaded.cloud_nio.org.threeten.bp.Duration;</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"> /**</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -49,33 +43,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> class GoogleStorageUtils {</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"> public static void initialize() {</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CloudStorageFileSystemProvider.setDefaultCloudStorageConfiguration(GoogleStorageUtils.getCloudStorageConfiguration(20));</span></span>
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21
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- CloudStorageFileSystemProvider.setStorageOptions(GoogleStorageUtils.setGenerousTimeouts(StorageOptions.newBuilder()).build());</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> }</span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </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;">- /** The config we want to use. **/</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;">- private static CloudStorageConfiguration getCloudStorageConfiguration(int maxReopens) {</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;">- return CloudStorageConfiguration.builder()</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- // if the channel errors out, re-open up to this many times</span></span>
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28
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- .maxChannelReopens(maxReopens)</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;">- .build();</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;">- }</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;">-</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;">- private static StorageOptions.Builder setGenerousTimeouts(StorageOptions.Builder builder) {</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return builder</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- .setTransportOptions(HttpTransportOptions.newBuilder()</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;">- .setConnectTimeout(120_000)</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;">- .setReadTimeout(120_000)</span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- .build())</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;">- .setRetrySettings(RetrySettings.newBuilder()</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;">- .setMaxAttempts(15)</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;">- .setMaxRetryDelay(Duration.ofMillis(256_000L))</span></span>
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41
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- .setTotalTimeout(Duration.ofMillis(4000_000L))</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- .setInitialRetryDelay(Duration.ofMillis(1000L))</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;">- .setRetryDelayMultiplier(2.0)</span></span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- .setInitialRpcTimeout(Duration.ofMillis(180_000L))</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;">- .setRpcTimeoutMultiplier(1.0)</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;">- .setMaxRpcTimeout(Duration.ofMillis(180_000L))</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;">- .build());</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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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> }</span></pre>
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<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,3 +2,6 @@</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">20-shadowjar.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">30-tests-fix-dataprovider.patch</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">40-tests-fix-testng.patch</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">remove_google_nio.patch</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="plaintext">fix_javadoc_ascii.patch</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">fix_test_freezing</span></pre>
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<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#5fc71f47ab3e62ea5e6c822e31df70828d788474"><strong>debian/pom-picard.xml</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">@@ -31,9 +31,19 @@</td>
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<pre style="margin: 0;"> <span id="LC31" class="line" lang="xml"> <span class="nt" style="color: navy;"></developers></span></span>
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<pre style="margin: 0;"> <span id="LC32" class="line" lang="xml"> <span class="nt" style="color: navy;"><dependencies></span></span>
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<pre style="margin: 0;"> <span id="LC33" class="line" lang="xml"> <span class="nt" style="color: navy;"><dependency></span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="xml"> <span class="nt" style="color: navy;"><groupId></span>org.broadinstitute<span class="nt" style="color: navy;"></groupId></span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="xml"> <span class="nt" style="color: navy;"><artifactId></span>barclay<span class="nt" style="color: navy;"></artifactId></span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="xml"> <span class="nt" style="color: navy;"><version></span>debian<span class="nt" style="color: navy;"></version></span></span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="xml"> <span class="nt" style="color: navy;"></dependency></span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="xml"> <span class="nt" style="color: navy;"><dependency></span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="xml"> <span class="nt" style="color: navy;"><groupId></span>org.apache.commons<span class="nt" style="color: navy;"></groupId></span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="xml"> <span class="nt" style="color: navy;"><artifactId></span>commons-lang3<span class="nt" style="color: navy;"></artifactId></span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="xml"> <span class="nt" style="color: navy;"><version></span>debian<span class="nt" style="color: navy;"></version></span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="xml"> <span class="nt" style="color: navy;"></dependency></span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="xml"> <span class="nt" style="color: navy;"><dependency></span></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="xml"> <span class="nt" style="color: navy;"><groupId></span>com.github.samtools<span class="nt" style="color: navy;"></groupId></span></span>
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45
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="xml"> <span class="nt" style="color: navy;"><artifactId></span>htsjdk<span class="nt" style="color: navy;"></artifactId></span></span>
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<pre style="margin: 0;">-<span id="LC36" class="line" lang="xml"> <span class="nt" style="color: navy;"><version></span><span class="idiff left right">2.1.1</span><span class="nt" style="color: navy;"></version></span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="xml"> <span class="nt" style="color: navy;"><version></span><span class="idiff left right">debian</span><span class="nt" style="color: navy;"></version></span></span>
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<pre style="margin: 0;"> <span id="LC47" class="line" lang="xml"> <span class="nt" style="color: navy;"></dependency></span></span>
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<pre style="margin: 0;"> <span id="LC48" class="line" lang="xml"> <span class="nt" style="color: navy;"><dependency></span></span>
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<pre style="margin: 0;"> <span id="LC49" class="line" lang="xml"> <span class="nt" style="color: navy;"><groupId></span>com.google.cloud.genomics<span class="nt" style="color: navy;"></groupId></span></span>
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<li id="8756c63497c8dc39f7773438edf53b220c773f67">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/4b83bd878593af08af753b088df7c952d0a701ee...79c845f232139bee8ce68bab4edcdfd063ee7b08#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">@@ -9,6 +9,10 @@ export JAVA_HOME=$(readlink -f /usr/bin/javac | sed "s:/bin/javac::")</td>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="plaintext">%:</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext"> dh $@ --buildsystem=gradle --with javahelper,jh_maven_repo_helper</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext">override_dh_link:</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext"> rm -f debian/libpicard-java-doc/usr/share/doc/libpicard-java/api/jquery/external/jquery/jquery.js</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="plaintext"> dh_link</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext">override_dh_auto_build:</span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> dh_auto_build -- jar javadoc</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="16" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -16,8 +20,8 @@ override_dh_auto_test:</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"> # Tests do not work with locales with a different decimal separator</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> # (for example ',') </span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> env LC_ALL=C \</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> # disable unit tests waiting for <span class="idiff left right">gradle 3.4 update in debian</span></span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> #dh_auto_build -- test</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> # disable unit tests waiting for <span class="idiff left right">testng fix in jcommander not found</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> #<span class="idiff left right"> </span>dh_auto_build -- test</span>
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21
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"></span>
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<td class="diff-line-num old_line" data-linenumber="22" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
22
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext">override_dh_clean:</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> dh_clean</span>
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