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<h3>
Andreas Tille 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/a8d4603e76197ac6fad396efaf00e2d5fa6eae81">a8d4603e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-12T07:23:23Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Try to exclude failing test but this is not the right one. :-(
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/commit/08962e056deb57731772e703a5731c64b8ba8c8f">08962e05</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-12T07:27:16Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Close bug
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/commit/f5acfe53f75c912d0f3f9c90153f535a7f67ae65">f5acfe53</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-12T07:57:32Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">DEP3
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/commit/30cb011a9817e57aa0644867fb19625357e92a4f">30cb011a</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-12T08:06:35Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Add ALIGNMENT_STATUS=All to command line
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/commit/5c2de50991138588ab4e36be161bdcf528a47d0a">5c2de509</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2018-12-12T08:23:17Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Upload to unstable
</pre>
</li>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
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<li class="file-stats">
<a href="#4c28a8ec31f904862c75ca6cdb725c2cba7bae50">
<span class="new-file">
+
debian/patches/50-tests-exclude-Barclay.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/c29ce28b0c83184c89a587967558f5f642761724...5c2de50991138588ab4e36be161bdcf528a47d0a#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">picard-tools (2.18.17+dfsg-1) <span class="idiff left right">UNRELEASED</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">picard-tools (2.18.17+dfsg-1) <span class="idiff left right">unstable</span>; urgency=medium</span>
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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="LC2" class="line" lang="plaintext"></span>
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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="LC3" class="line" lang="plaintext"> [ Emmanuel Bourg ]</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> * Team upload.</span>
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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"> * Fixed the build failure with Java 11</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext"> Closes: #915898, #880258</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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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="LC7" class="line" lang="plaintext"> [ Andreas Tille ]</span>
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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="LC8" class="line" lang="plaintext"> * New upstream version</span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="10" 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="10" 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">@@ -10,8 +10,10 @@ picard-tools (2.18.17+dfsg-1) UNRELEASED; urgency=medium</td>
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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="LC10" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog</span>
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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">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext"> * Remove trailing whitespace in debian/control</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext"> * Remove trailing whitespace in debian/rules</span>
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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(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="13" style="width: 35px; color: rgba(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="LC13" class="line" lang="plaintext"> * Add ALIGNMENT_STATUS=All to command line</span>
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<td class="diff-line-num new old_line" data-linenumber="13" style="width: 35px; color: rgba(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="LC14" class="line" lang="plaintext"> Closes: #905645</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="LC14" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Sat, 01 Dec 2018 08:03:1</span>7 +0100</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> <span class="idiff left right">Wed, 12 Dec 2018 09:06:3</span>7 +0100</span>
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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">picard-tools (2.18.14+dfsg-1) unstable; urgency=medium</span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="plaintext"></span>
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<a href="https://salsa.debian.org/med-team/picard-tools/compare/c29ce28b0c83184c89a587967558f5f642761724...5c2de50991138588ab4e36be161bdcf528a47d0a#4c28a8ec31f904862c75ca6cdb725c2cba7bae50"><strong>debian/patches/50-tests-exclude-Barclay.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Author: Andreas Tille <tille@debian.org></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Last-Update: Sat, 01 Dec 2018 08:03:17 +0100</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Description: There used to be a tes suite error with BarclayParser</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> and so this test was excluded. It turned out that the error does</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff"> not occur under all circumstances - may be this patch can/should be</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"> deleted.</span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"> .</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> FIXME: Try next release without this patch</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/test/java/picard/cmdline/PicardCommandLineTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/test/java/picard/cmdline/PicardCommandLineTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -37,30 +37,9 @@ public class PicardCommandLineTest {</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"> // NOTE that it does NOT test that those tools actually work correctly, only that they aren't immediately</span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> // rejected with a CommandLineParserInternalException from the Barclay parser.</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;">- @Test</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;">- public void testLaunchAllCommandLineProgramsWithBarclayParser() {</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;">- PicardCommandLine.processAllCommandLinePrograms(</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;">- Collections.singletonList("picard"),</span></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;">- (Class<CommandLineProgram> clazz, CommandLineProgramProperties clProperties) -> {</span></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;">- // Check for missing annotations</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- if (null != clProperties) {</span></span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- try {</span></span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Object commandLineProgram = clazz.newInstance();</span></span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- try {</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;">- new CommandLineArgumentParser(commandLineProgram);</span></span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } catch (CommandLineException.CommandLineParserInternalException e) {</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw new RuntimeException("Barclay command line parser internal exception parsing class: " + clazz.getName(), e);</span></span>
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<pre style="margin: 0;">+<span id="LC29" 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="LC30" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } catch (IllegalAccessException | InstantiationException e) {</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;">- throw new RuntimeException("Failure instantiating command line program: " + clazz.getName(), e);</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;">- }</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;">- }</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;">- }</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;">- );</span></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"> @Test</span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> public void testPrintUsage() {</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"> Assert.assertEquals(new PicardCommandLine().instanceMain(new String[]{"-h"}), 1);</span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"> }</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;">-}</span></span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff">\ No newline at end of file</span>
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+}</span></span></pre>
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<a href="https://salsa.debian.org/med-team/picard-tools/compare/c29ce28b0c83184c89a587967558f5f642761724...5c2de50991138588ab4e36be161bdcf528a47d0a#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">@@ -2,5 +2,6 @@</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="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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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext">40-tests-fix-testng.patch</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">50-tests-exclude-Barclay.patch</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">remove_google_nio.patch</span>
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">fix_javadoc_ascii.patch</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/c29ce28b0c83184c89a587967558f5f642761724...5c2de50991138588ab4e36be161bdcf528a47d0a#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="14" 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="14" 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">@@ -14,9 +14,7 @@ cp -a /usr/share/doc/${pkg}/test.* .</td>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: teal;">pkg</span><span class="k" style="font-weight: 600;">}</span>/mini.vcf<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="shell"><span class="nb" style="color: #0086b3;">gunzip</span> <span class="nt" style="color: navy;">-r</span> <span class="k" style="font-weight: 600;">*</span></span>
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<pre style="margin: 0;"> <span id="LC16" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC17" class="line" lang="shell"><span class="nb" style="color: #0086b3;">set</span> <span class="nt" style="color: navy;">-x</span></span>
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<pre style="margin: 0;">-<span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;">-<span id="LC19" class="line" lang="shell">PicardCommandLine ViewSam <span class="nv" style="color: teal;">INPUT</span><span class="o" style="font-weight: 600;">=</span>unmapped.sam</span>
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="shell">PicardCommandLine ViewSam <span class="nv" style="color: teal;">ALIGNMENT_STATUS</span><span class="o" style="font-weight: 600;">=</span>All <span class="nv" style="color: teal;">INPUT</span><span class="o" style="font-weight: 600;">=</span>unmapped.sam</span>
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<pre style="margin: 0;"> <span id="LC18" class="line" lang="shell"></span>
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<pre style="margin: 0;"> <span id="LC19" class="line" lang="shell">PicardCommandLine CollectSequencingArtifactMetrics <span class="nv" style="color: teal;">I</span><span class="o" style="font-weight: 600;">=</span>test.sam <span class="nv" style="color: teal;">O</span><span class="o" style="font-weight: 600;">=</span><span class="nb" style="color: #0086b3;">test </span><span class="nv" style="color: teal;">R</span><span class="o" style="font-weight: 600;">=</span>test.fasta</span>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="shell"></span>
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