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<h3>
Olivier Sallou pushed to branch master
at <a href="https://salsa.debian.org/med-team/htsjdk">Debian Med / htsjdk</a>
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<h4>
Commits:
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<ul>
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<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/3000bdb26eee29af66b02edab243ad834a2c60e0">3000bdb2</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2018-04-17T12:21:15+00:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">reintroduce tests
</pre>
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<h4>5 changed files:</h4>
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<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#52b48dcfaeb86a97b0a2e932ab203797ce0ef59c">
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+
debian/patches/60-enable-tests
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<li class="file-stats">
<a href="#1829ef4ce68fdf0343d52cba28050f16f50ac5d0">
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+
debian/patches/70-removesometests-testng.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#8756c63497c8dc39f7773438edf53b220c773f67">
debian/rules
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/htsjdk/commit/3000bdb26eee29af66b02edab243ad834a2c60e0#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="17" 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">@@ -17,10 +17,10 @@ htsjdk (2.14.3+dfsg-1) UNRELEASED-targeting-experimental; urgency=medium</td>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext"> </span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="plaintext"> [TODO - O. Sallou in progress]</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> * Reintroduce unit tests now that gradle 3.4 is available in sid</span>
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<pre style="margin: 0;">-<span id="LC20" class="line" lang="plaintext"> - <span class="idiff left right">new patch is nee</span>ded for latest upstream, referencing junit classes</span>
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<pre style="margin: 0;">-<span id="LC21" class="line" lang="plaintext"> - <span class="idiff left right">ad</span>d testng() call in build.gradle with a patch and set test call in d/rules back</span>
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<pre style="margin: 0;">-<span id="LC22" class="line" lang="plaintext"> - testng fails now with jcommander classnotfound exception<span class="idiff left right"> (was working before),</span></span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="plaintext"> <span class="idiff left right">may need to add dependency in testCompile of build.gradle, don't understand the reason (testng depends on it, but gradle does not find it)</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="plaintext"> - <span class="idiff left right">[done] new patch ad</span>ded for latest upstream, referencing junit classes</span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="plaintext"> - <span class="idiff left right">[done] adde</span>d testng() call in build.gradle with a patch and set test call in d/rules back</span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="plaintext"> - testng fails now with jcommander classnotfound exception<span class="idiff left right">, this is a testng bug</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="plaintext"> <span class="idiff left right">(#895886: testng: jcommander classes not found), wait to be fixed to enable tests in d/rules</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Wed, 28 Mar 2018 14:19:04 +0200</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"></span>
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<li id="52b48dcfaeb86a97b0a2e932ab203797ce0ef59c">
<a href="https://salsa.debian.org/med-team/htsjdk/commit/3000bdb26eee29af66b02edab243ad834a2c60e0#52b48dcfaeb86a97b0a2e932ab203797ce0ef59c"><strong>debian/patches/60-enable-tests</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="mosel"><span class="p">---</span> <span class="n" style="color: #333;">a</span><span class="p">/</span><span class="n" style="color: #333;">build</span><span class="p">.</span><span class="n" style="color: #333;">gradle</span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="mosel"><span class="p">+++</span> <span class="n" style="color: #333;">b</span><span class="p">/</span><span class="n" style="color: #333;">build</span><span class="p">.</span><span class="n" style="color: #333;">gradle</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="mosel"><span class="p">@@</span> <span class="p">-</span><span class="m" style="color: #099;">86</span><span class="p">,</span><span class="m" style="color: #099;">9</span> <span class="p">+</span><span class="m" style="color: #099;">86</span><span class="p">,</span><span class="m" style="color: #099;">14</span> <span class="p">@@</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="mosel"> <span class="n" style="color: #333;">events</span> <span class="s2" style="color: #d14;">"failed"</span><span class="p">,</span> <span class="s2" style="color: #d14;">"skipped"</span></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="mosel"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="mosel"> </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">
7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="mosel"><span class="p">+</span> <span class="n" style="color: #333;">useTestNG</span><span class="p">()</span></span>
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<td class="diff-line-num new new_line" data-linenumber="8" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="mosel"><span class="p">+</span> <span class="n" style="color: #333;">minHeapSize</span> <span class="p">=</span> <span class="s2" style="color: #d14;">"1G"</span></span>
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<td class="diff-line-num new new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
9
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="mosel"><span class="p">+</span> <span class="n" style="color: #333;">maxHeapSize</span> <span class="p">=</span> <span class="s2" style="color: #d14;">"2G"</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="mosel"><span class="p">+</span></span>
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<td class="diff-line-num new new_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">if</span> <span class="p">(</span><span class="nf" style="color: #900; font-weight: 600;">System</span><span class="p">.</span><span class="n" style="color: #333;">env</span><span class="p">.</span><span class="n" style="color: #333;">CI</span> <span class="p">==</span> <span class="s2" style="color: #d14;">"true"</span><span class="p">)</span> <span class="p">{</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="mosel"> <span class="n" style="color: #333;">jvmArgs</span> <span class="p">+=</span> <span class="s1" style="color: #d14;">'-Dsamjdk.sra_libraries_download=true'</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="mosel"> <span class="p">}</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="mosel"><span class="p">+</span> <span class="n" style="color: #333;">jvmArgs</span> <span class="p">+=</span> <span class="p">[</span><span class="s2" style="color: #d14;">"--add-modules"</span><span class="p">,</span> <span class="s2" style="color: #d14;">"java.xml.bind"</span><span class="p">]</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="mosel"> </span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="mosel"> <span class="n" style="color: #333;">exclude</span> <span class="s1" style="color: #d14;">'htsjdk/samtools/sra/**'</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="mosel"> <span class="n" style="color: #333;">exclude</span> <span class="s1" style="color: #d14;">'htsjdk/samtools/BAMFileIndexTest.java'</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="mosel"><span class="p">---</span> <span class="n" style="color: #333;">a</span><span class="p">/</span><span class="n" style="color: #333;">src</span><span class="p">/</span><span class="n" style="color: #333;">test</span><span class="p">/</span><span class="n" style="color: #333;">java</span><span class="p">/</span><span class="n" style="color: #333;">htsjdk</span><span class="p">/</span><span class="n" style="color: #333;">utils</span><span class="p">/</span><span class="n" style="color: #333;">ClassFinderTest</span><span class="p">.</span><span class="n" style="color: #333;">java</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="mosel"><span class="p">+++</span> <span class="n" style="color: #333;">b</span><span class="p">/</span><span class="n" style="color: #333;">src</span><span class="p">/</span><span class="n" style="color: #333;">test</span><span class="p">/</span><span class="n" style="color: #333;">java</span><span class="p">/</span><span class="n" style="color: #333;">htsjdk</span><span class="p">/</span><span class="n" style="color: #333;">utils</span><span class="p">/</span><span class="n" style="color: #333;">ClassFinderTest</span><span class="p">.</span><span class="n" style="color: #333;">java</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="mosel"><span class="p">@@</span> <span class="p">-</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="m" style="color: #099;">7</span> <span class="p">+</span><span class="m" style="color: #099;">1</span><span class="p">,</span><span class="m" style="color: #099;">7</span> <span class="p">@@</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="mosel"> <span class="k" style="font-weight: 600;">package</span> <span class="n" style="color: #333;">htsjdk</span><span class="p">.</span><span class="n" style="color: #333;">utils</span><span class="p">;</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="mosel"> </span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="mosel"> <span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">htsjdk</span><span class="p">.</span><span class="n" style="color: #333;">HtsjdkTest</span><span class="p">;</span></span>
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<td class="diff-line-num new new_line" data-linenumber="24" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="mosel"><span class="p">-</span><span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">org</span><span class="p">.</span><span class="n" style="color: #333;">junit</span><span class="p">.</span><span class="n" style="color: #333;">Assert</span><span class="p">;</span></span>
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25
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="mosel"><span class="p">+</span><span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">org</span><span class="p">.</span><span class="n" style="color: #333;">testng</span><span class="p">.</span><span class="n" style="color: #333;">Assert</span><span class="p">;</span></span>
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26
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="mosel"> <span class="n" style="color: #333;">import</span> <span class="n" style="color: #333;">org</span><span class="p">.</span><span class="n" style="color: #333;">testng</span><span class="p">.</span><span class="n" style="color: #333;">annotations</span><span class="p">.</span><span class="n" style="color: #333;">Test</span><span class="p">;</span></span>
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27
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="mosel"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="mosel"> <span class="p">/**</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="mosel"><span class="p">@@</span> <span class="p">-</span><span class="m" style="color: #099;">28</span><span class="p">,</span><span class="m" style="color: #099;">4</span> <span class="p">+</span><span class="m" style="color: #099;">28</span><span class="p">,</span><span class="m" style="color: #099;">4</span> <span class="p">@@</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="mosel"> <span class="n" style="color: #333;">Assert</span><span class="p">.</span><span class="n" style="color: #333;">assertEquals</span><span class="p">(</span><span class="n" style="color: #333;">finder</span><span class="p">.</span><span class="n" style="color: #333;">getClasses</span><span class="p">().</span><span class="n" style="color: #333;">stream</span><span class="p">()</span></span>
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31
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="mosel"> <span class="p">.</span><span class="n" style="color: #333;">filter</span><span class="p">(</span><span class="n" style="color: #333;">c</span> <span class="p">-></span> <span class="n" style="color: #333;">c</span><span class="p">.</span><span class="n" style="color: #333;">getName</span><span class="p">().</span><span class="n" style="color: #333;">equals</span><span class="p">(</span><span class="s2" style="color: #d14;">"htsjdk.utils.ClassFinder"</span><span class="p">)).</span><span class="k" style="font-weight: 600;">count</span><span class="p">(),</span> <span class="m" style="color: #099;">1</span><span class="p">);</span></span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="mosel"> <span class="p">}</span></span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="mosel"><span class="p">-}</span></span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="mosel"><span class="p">\</span> <span class="n" style="color: #333;">No</span> <span class="n" style="color: #333;">newline</span> <span class="n" style="color: #333;">at</span> <span class="k" style="font-weight: 600;">end</span> <span class="k" style="font-weight: 600;">of</span> <span class="n" style="color: #333;">file</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="mosel"><span class="p">+}</span></span></pre>
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<li id="1829ef4ce68fdf0343d52cba28050f16f50ac5d0">
<a href="https://salsa.debian.org/med-team/htsjdk/commit/3000bdb26eee29af66b02edab243ad834a2c60e0#1829ef4ce68fdf0343d52cba28050f16f50ac5d0"><strong>debian/patches/70-removesometests-testng.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Subject: testng issue with auto parameter mapping</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Description: testng below or equal to 6.9.13.4 does nto correctly map</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> long and Integers. This leads to test issues when provider [0,9] values</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> and methods expects a long (testng sends an Integer).</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> This patch disable some tests around this</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff">Author: Olivier Sallou <osallou@debian.org></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff">Forwarded: Not-Needed</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff">Last-Updated: 2018-02-19</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;">--- a/src/test/java/htsjdk/samtools/SAMIntegerTagTest.java</span></span>
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10
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/test/java/htsjdk/samtools/SAMIntegerTagTest.java</span></span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -296,11 +296,11 @@</span></span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> List<Object[]> params = new ArrayList<Object[]>();</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> for (FORMAT format:FORMAT.values()) {</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> for (ValidationStringency stringency:ValidationStringency.values()) {</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- params.add(new Object[]{0, format, stringency});</span></span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- params.add(new Object[]{1, format, stringency});</span></span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- params.add(new Object[]{-1, format, stringency});</span></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;">- params.add(new Object[]{Integer.MIN_VALUE, format, stringency});</span></span>
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- params.add(new Object[]{Integer.MAX_VALUE, format, stringency});</span></span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //params.add(new Object[]{0, format, stringency});</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //params.add(new Object[]{1, format, stringency});</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //params.add(new Object[]{-1, format, stringency});</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //params.add(new Object[]{Integer.MIN_VALUE, format, stringency});</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ //params.add(new Object[]{Integer.MAX_VALUE, format, stringency});</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> params.add(new Object[]{1L, format, stringency});</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> params.add(new Object[]{-1L, format, stringency});</span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/test/java/htsjdk/samtools/filter/IntervalKeepPairFilterTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -115,10 +115,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> intervalList_unmapped.add(interval);</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"> return new Object[][]{</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;">- {intervalList_twoPair, 4},</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;">- {intervalList_noMatch, 0},</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;">- {intervalList_onePair, 2},</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;">- {intervalList_unmapped, 4}</span></span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ {intervalList_twoPair, 4L},</span></span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ {intervalList_noMatch, 0L},</span></span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ {intervalList_onePair, 2L},</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ {intervalList_unmapped, 4L}</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> };</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"> }</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;">--- a/src/test/java/htsjdk/samtools/seekablestream/SeekableStreamGZIPinputStreamIntegrationTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/test/java/htsjdk/samtools/seekablestream/SeekableStreamGZIPinputStreamIntegrationTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -118,6 +118,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> return data.iterator();</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ /*</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> @Test(dataProvider = "compressedVcfsToTest")</span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> public void testWrappedSeekableStreamInGZIPinputStream(final File input, final long nLines) throws Exception {</span>
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54
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"> try (final LineReader reader = new BufferedLineReader(new GZIPInputStream(new SeekableFileStream(input)))) {</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -126,9 +127,10 @@</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> Assert.assertNull(reader.readLine());</span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"> Assert.assertEquals(reader.getLineNumber(), nLines);</span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ */</span></span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ /*</span></span>
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> @Test(dataProvider = "compressedVcfsToTest")</span>
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> public void testConsistencyWithBgzip(final File input, final long nLines) throws Exception {</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> try (final InputStream gzIs = new GZIPInputStream(new SeekableFileStream(input));</span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -139,7 +141,7 @@</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> bgz = bgzIs.read();</span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> }</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> Assert.assertEquals(gzIs.read(), bgz);</span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</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 class="gi" style="color: #000; background-color: #dfd;">+ */</span></span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> }</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;">--- a/src/test/java/htsjdk/samtools/util/GZIIndexTest.java</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/test/java/htsjdk/samtools/util/GZIIndexTest.java</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -110,6 +110,7 @@</span></span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> return data.iterator();</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> }</span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"> </span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ /*</span></span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> @Test(dataProvider = "virtualOffsetForSeekData")</span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> public void testGetVirtualOffsetForSeek(final long uncompressedOffset,</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> final long expectedBlockAddress, final long expectedBlockOffset,</span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -118,5 +119,6 @@</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> Assert.assertEquals(BlockCompressedFilePointerUtil.getBlockAddress(virtualOffset), expectedBlockAddress);</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> Assert.assertEquals(BlockCompressedFilePointerUtil.getBlockOffset(virtualOffset), expectedBlockOffset);</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ */</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff">\ No newline at end of file</span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/htsjdk/commit/3000bdb26eee29af66b02edab243ad834a2c60e0#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<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">@@ -4,3 +4,5 @@</td>
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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">30-disable-scalatest.patch</span>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">40-fix-java9</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">50-fix-javadoc</span>
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7
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="plaintext">60-enable-tests</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">70-removesometests-testng.patch</span></pre>
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<a href="https://salsa.debian.org/med-team/htsjdk/commit/3000bdb26eee29af66b02edab243ad834a2c60e0#8756c63497c8dc39f7773438edf53b220c773f67"><strong>debian/rules</strong></a>
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<td class="diff-line-num unfold js-unfold 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">...</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">@@ -15,8 +15,7 @@ override_dh_auto_build:</td>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext"> dh_auto_build -- jar javadoc</span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC17" class="line" lang="plaintext">override_dh_auto_test:</span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="plaintext"> # Bug 877590: gradle 3.2 fails to execute tests, disable unit testing</span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="plaintext"> # waiting for gradle 3.4 availability</span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="plaintext"> # testng bug 895886: testng: jcommander classes not found</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"> # dh_auto_build -- test</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext">override_jh_installlibs:</span>
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