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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/a8f248ceee196765fd0c4adb68f3fd7a47ea05ac">a8f248ce</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2019-01-17T17:58:22Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">add PF_STATUS to test
</pre>
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<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/commit/b5887cee88ee8a326fa4ce0ff35be89d661cd5bd">b5887cee</a></strong>
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<span>by Olivier Sallou</span>
<i>at 2019-01-18T14:12:11Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove failing tests with autopkgtests, due to root access
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<h4>4 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="#2338e60d4382624824f4ac493301417b621e0a9d">
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+
debian/patches/fix_unreadabletests.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="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
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<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/c93e1866f9549e899c8ce00549e94bd3b53f1804...b5887cee88ee8a326fa4ce0ff35be89d661cd5bd#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">picard-tools (2.18.23+dfsg-2) <span class="idiff left right">UNRELEASE</span>; urgency=medium</span>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="plaintext">picard-tools (2.18.23+dfsg-2) <span class="idiff left right">unstable</span>; urgency=medium</span>
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<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"> * Fix Class-Path in manifest file for dependencies (Closes: #919559).</span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> [TODO] 2 tests are still failing with autopkgtest though source build</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> and testing works fine.</span>
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"></span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> -- Olivier Sallou <osallou@debian.org> Thu, 17 Jan 2019 15:54:27 +0000</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<li id="2338e60d4382624824f4ac493301417b621e0a9d">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/c93e1866f9549e899c8ce00549e94bd3b53f1804...b5887cee88ee8a326fa4ce0ff35be89d661cd5bd#2338e60d4382624824f4ac493301417b621e0a9d"><strong>debian/patches/fix_unreadabletests.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Subject: tests on unreadable fail</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Description: some tests try to check that a non readable file or directory</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"> is correctly managed. However during Debian build, sometimes user is root</span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"> and unreadable is not effective. This patch removes related tests</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Last-Updated: 2019-01-18</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: no</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;">--- a/src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -155,33 +155,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> Assert.assertEquals(metricsFile.getMetrics().get(12).PERFECT_MATCHES, 1);</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"> }</span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> </span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @Test</span></span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void testNonWritableOutputFile() throws Exception {</span></span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final File existingFile = new File(basecallsDir, "s_1_1101_barcode.txt.gz");</span></span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- try {</span></span>
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18
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- existingFile.setReadOnly();</span></span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final String readStructure = "25T8B25T";</span></span>
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20
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final int lane = 1;</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;">-</span></span>
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22
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final File metricsFile = File.createTempFile("eib.", ".metrics");</span></span>
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23
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- metricsFile.deleteOnExit();</span></span>
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24
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</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;">- final List<String> args = new ArrayList<>(Arrays.asList(</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;">- "BASECALLS_DIR=" + basecallsDir.getPath(),</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;">- "LANE=" + lane,</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;">- "READ_STRUCTURE=" + readStructure,</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;">- "METRICS_FILE=" + metricsFile.getPath(),</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;">- "COMPRESS_OUTPUTS=true"</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;">- for (final String barcode : BARCODES) {</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;">- args.add("BARCODE=" + barcode);</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;">- Assert.assertEquals(runPicardCommandLine(args), 4);</span></span>
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36
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } finally {</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;">- existingFile.setWritable(true);</span></span>
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<pre style="margin: 0;">+<span id="LC38" 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="LC39" 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="LC40" 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="LC41" class="line" lang="diff"> </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"> * 4 cases tested:</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;">--- a/src/test/java/picard/util/LiftoverVcfTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/test/java/picard/util/LiftoverVcfTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -1196,30 +1196,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> Assert.assertEquals(runPicardCommandLine(args), 1);</span>
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @Test(expectedExceptions = SAMException.class, expectedExceptionsMessageRegExp = "File exists but is not readable:.*")</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void testUnreadableDictionary() throws IOException {</span></span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Path liftOutput = Files.createTempFile("tmpouput", ".vcf");</span></span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- liftOutput.toFile().deleteOnExit();</span></span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Path rejectOutput = Files.createTempFile("tmpreject", ".vcf");</span></span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- rejectOutput.toFile().deleteOnExit();</span></span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Path input = TEST_DATA_PATH.toPath().resolve("testLiftoverBiallelicIndels.vcf");</span></span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Path tmpCopyDir = Files.createTempDirectory("copy");</span></span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- tmpCopyDir.toFile().deleteOnExit();</span></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;">- final Path referenceCopy = tmpCopyDir.resolve("refCopy.fasta");</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- referenceCopy.toFile().deleteOnExit();</span></span>
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61
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Files.copy(REFERENCE_FILE.toPath(), referenceCopy);</span></span>
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62
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Path dictCopy = referenceCopy.resolveSibling(referenceCopy.toFile().getName().replaceAll("fasta$", "dict"));</span></span>
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63
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dictCopy.toFile().deleteOnExit();</span></span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final Path dictionary = REFERENCE_FILE.toPath().resolveSibling(REFERENCE_FILE.getName().replaceAll("fasta$", "dict"));</span></span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Files.copy(dictionary, dictCopy);</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- dictCopy.toFile().setReadable(false);</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final String[] args = new String[]{</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "INPUT=" + input,</span></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;">- "OUTPUT=" + liftOutput,</span></span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "REJECT=" + rejectOutput,</span></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;">- "CHAIN=" + CHAIN_FILE,</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- "REFERENCE_SEQUENCE=" + referenceCopy,</span></span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- };</span></span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- runPicardCommandLine(args);</span></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;">- }</span></span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"> }</span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/c93e1866f9549e899c8ce00549e94bd3b53f1804...b5887cee88ee8a326fa4ce0ff35be89d661cd5bd#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="diff-line-num unfold js-unfold new_line" data-linenumber="5" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">...</td>
<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,3 +5,4 @@</td>
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5
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5
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext">50-tests-exclude-Barclay.patch</span>
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6
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6
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext">remove_google_nio.patch</span>
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7
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7
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="plaintext">fix_javadoc_ascii.patch</span>
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8
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext">fix_unreadabletests.patch</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/picard-tools/compare/c93e1866f9549e899c8ce00549e94bd3b53f1804...b5887cee88ee8a326fa4ce0ff35be89d661cd5bd#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">@@ -14,7 +14,7 @@ cp -a /usr/share/doc/${pkg}/test.* .</td>
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14
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14
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: navy;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</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">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="LC17" class="line" lang="shell">PicardCommandLine ViewSam <span class="nv" style="color: teal;"><span class="idiff left">PF_STATUS</span></span><span class="o" style="font-weight: 600;"><span class="idiff">=</span></span><span class="idiff right">All </span><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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