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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/8c0956505fa06c6477d3ac8bacf9fb55d0714eae">8c095650</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2020-06-16T06:03:11+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove google.nio ref
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/f2a21c201254663a531e63c7e85c469eeb8bf741">f2a21c20</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2020-06-16T06:04:27+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove google.nio ref
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/50b9595b3514dc4b94e9d424080e77bfd56d6fcb">50b9595b</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2020-06-16T06:06:00+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove google.nio ref
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/fc0d3131c83bbafbd3e341073534f26825a49234">fc0d3131</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2020-06-16T06:19:20+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove tests with dataprovider errors
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/7f4782faff7969473aaf62d767bcc345fe64ad3c">7f4782fa</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2020-06-16T06:44:15+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">new upstream release 2.22.8 with related htsjdk
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/picard-tools/-/commit/7e6e04739bba5aa27566e9f888b0a04becb75021">7e6e0473</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2020-06-16T06:52:50+00:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove deprecated ADTTMP, replace by AUTOPKGTEST_TMP
</pre>
</li>
</ul>
<h4>5 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
debian/control
</a>
</li>
<li class="file-stats">
<a href="#4416da23ca69dd7403c07c230b77bb0c32e0abb1">
debian/patches/30-tests-fix-dataprovider.patch
</a>
</li>
<li class="file-stats">
<a href="#a19ab181f42f2952911fb425a841f9a77adf945f">
debian/patches/remove_google_nio.patch
</a>
</li>
<li class="file-stats">
<a href="#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
debian/tests/run-unit-test
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/picard-tools/-/compare/44ca3a8617a0d04c16876db768e305f4f086354f...7e6e04739bba5aa27566e9f888b0a04becb75021#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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<pre style="margin: 0;">-<span id="LC1" class="line" lang="plaintext">picard-tools (2.22.8+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 (2.22.8+dfsg-1) <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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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext"> * New upstream release </span>
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<pre style="margin: 0;">-<span id="LC4" class="line" lang="plaintext"> [TODO]</span>
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="plaintext"> fails to compile, need new htsjdk version</span>
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="plaintext"> * New upstream release</span>
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<td class="diff-line-num old_line" data-linenumber="7" 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="LC4" class="line" lang="plaintext"> * Source only upload</span>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="plaintext"> Closes: #961865</span>
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"></span>
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<li id="58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2">
<a href="https://salsa.debian.org/med-team/picard-tools/-/compare/44ca3a8617a0d04c16876db768e305f4f086354f...7e6e04739bba5aa27566e9f888b0a04becb75021#58ef006ab62b83b4bec5d81fe5b32c3b4c2d1cc2"><strong>debian/control</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -21,7 +21,7 @@ Build-Depends: default-jdk (>= 2:1.9~),</td>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="plaintext"> libgkl-java,</span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="plaintext"> libgatk-native-bindings-java,</span>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="plaintext"># htsjdk and picard-tools are relased nearly together</span>
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<pre style="margin: 0;">-<span id="LC24" class="line" lang="plaintext"> libhtsjdk-java (>= 2.<span class="idiff left right">18.2</span>~),</span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="plaintext"> libhtsjdk-java (>= 2.<span class="idiff left right">22.0</span>~),</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="plaintext"># required for tests:</span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="plaintext"> testng (>= 6.9.10),</span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="plaintext"> r-base-core,</span>
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<li id="4416da23ca69dd7403c07c230b77bb0c32e0abb1">
<a href="https://salsa.debian.org/med-team/picard-tools/-/compare/44ca3a8617a0d04c16876db768e305f4f086354f...7e6e04739bba5aa27566e9f888b0a04becb75021#4416da23ca69dd7403c07c230b77bb0c32e0abb1"><strong>debian/patches/30-tests-fix-dataprovider.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -77,3 +77,62 @@ Author: Sascha Steinbiss <satta@debian.org></td>
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<pre style="margin: 0;"> <span id="LC77" class="line" lang="diff"> outfile.deleteOnExit();</span>
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<pre style="margin: 0;"> <span id="LC78" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC79" class="line" lang="diff"> final String[] args = new String[] {</span>
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/test/java/picard/util/IntervalListToolsTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/test/java/picard/util/IntervalListToolsTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="p">@@ -173,7 +173,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @Test(dataProvider = "actionAndTotalBasesWithUniqueData")</span></span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> public void testActionsWithUnique(final IntervalListTools.Action action, final long bases, final int intervals) throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> final IntervalList il = tester(action, false, true);</span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> Assert.assertEquals(il.getBaseCount(), bases, "unexpected number of bases found.");</span>
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/test/java/picard/fingerprint/FingerprintCheckerTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/test/java/picard/fingerprint/FingerprintCheckerTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"><span class="p">@@ -100,7 +100,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @Test(dataProvider = "checkFingerprintsVcfDataProvider")</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> public void testCheckFingerprintsVcf(final File vcfFile, final File genotypesFile, final String observedSampleAlias, final String expectedSampleAlias,</span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> final double llExpectedSample, final double llRandomSample, final double lodExpectedSample) throws IOException {</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> final Path indexedInputVcf = VcfTestUtils.createTemporaryIndexedVcfFromInput(vcfFile, "fingerprintcheckertest.tmp.").toPath();</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"><span class="p">@@ -122,7 +121,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> Assert.assertEquals(mr.getLOD(), lodExpectedSample, DELTA);</span>
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @Test(dataProvider = "checkFingerprintsVcfDataProvider")</span></span>
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> public void testFingerprintVcf(final File vcfFile, final File genotypesFile, final String observedSampleAlias, final String expectedSampleAlias,</span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> final double llExpectedSample, final double llRandomSample, final double lodExpectedSample) {</span>
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> final FingerprintChecker fpChecker = new FingerprintChecker(SUBSETTED_HAPLOTYPE_DATABASE_FOR_TESTING);</span>
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="p">@@ -131,7 +129,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> Assert.assertFalse(fp1.isEmpty());</span>
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @Test(dataProvider = "checkFingerprintsVcfDataProvider")</span></span>
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"> public void testFingerprintSwapEqual(final File vcfFile, final File genotypesFile, final String observedSampleAlias, final String expectedSampleAlias,</span>
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> final double llExpectedSample, final double llRandomSample, final double lodExpectedSample) {</span>
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> final FingerprintChecker fpChecker = new FingerprintChecker(SUBSETTED_HAPLOTYPE_DATABASE_FOR_TESTING);</span>
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"><span class="p">@@ -435,4 +432,4 @@</span></span>
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> VcfTestUtils.assertVcfFilesAreEqual(vcfOutput, vcfExpected);</span>
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-}</span></span>
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="err" style="color: #a61717; background-color: #e3d2d2;">\</span> No newline at end of file</span>
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<pre style="margin: 0;">+<span id="LC122" 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="LC123" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/test/java/picard/arrays/illumina/InfiniumDataFileTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/test/java/picard/arrays/illumina/InfiniumDataFileTest.java</span></span>
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"><span class="p">@@ -21,13 +21,11 @@</span></span>
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"> };</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> }</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> </span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @Test(dataProvider = "byteArrayToIntDataProvider")</span></span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"> public void testByteArrayToInt(byte[] bytes, int expectedValue) {</span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"> short value = (short) InfiniumDataFile.byteArrayToInt(bytes);</span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> Assert.assertEquals(value, expectedValue);</span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> }</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> </span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @Test(dataProvider = "byteArrayToIntDataProvider")</span></span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> public void testShortToByteArray(byte[] expectedBytes, int value) {</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> byte[] themBytes = InfiniumDataFile.shortToByteArray((short) value);</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> Assert.assertEquals(themBytes, expectedBytes);</span></pre>
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<li id="a19ab181f42f2952911fb425a841f9a77adf945f">
<a href="https://salsa.debian.org/med-team/picard-tools/-/compare/44ca3a8617a0d04c16876db768e305f4f086354f...7e6e04739bba5aa27566e9f888b0a04becb75021#a19ab181f42f2952911fb425a841f9a77adf945f"><strong>debian/patches/remove_google_nio.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -62,3 +62,27 @@ Description: Remove Google cloud storage</td>
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62
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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;">- .build());</span></span>
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63
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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;">- }</span></span>
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64
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64
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<pre style="margin: 0;"> <span id="LC64" class="line" lang="diff"> }</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;">--- a/src/main/java/picard/fingerprint/FingerprintChecker.java</span></span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/main/java/picard/fingerprint/FingerprintChecker.java</span></span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="p">@@ -24,7 +24,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> package picard.fingerprint;</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </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;">-import com.google.cloud.storage.contrib.nio.SeekableByteChannelPrefetcher;</span></span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+//import com.google.cloud.storage.contrib.nio.SeekableByteChannelPrefetcher;</span></span>
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> import htsjdk.samtools.SAMFileHeader;</span>
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> import htsjdk.samtools.SAMReadGroupRecord;</span>
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> import htsjdk.samtools.SAMRecord;</span>
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="p">@@ -458,11 +458,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> private static final Function<SeekableByteChannel, SeekableByteChannel> seekableChannelFunction = (chan) -> {</span>
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<pre style="margin: 0;">+<span id="LC80" 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="LC81" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- return SeekableByteChannelPrefetcher.addPrefetcher(1, chan);</span></span>
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- } catch (IOException e) {</span></span>
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- throw new RuntimeException("Trouble wrapping seekable stream with prefetcher.", e);</span></span>
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<pre style="margin: 0;">+<span id="LC84" 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="LC85" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ throw new RuntimeException("Trouble wrapping seekable stream with prefetcher.");</span></span>
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> /**</span></pre>
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<li id="8c77cc51b09ef1f7b294222180bcdb53ebb70e2f">
<a href="https://salsa.debian.org/med-team/picard-tools/-/compare/44ca3a8617a0d04c16876db768e305f4f086354f...7e6e04739bba5aa27566e9f888b0a04becb75021#8c77cc51b09ef1f7b294222180bcdb53ebb70e2f"><strong>debian/tests/run-unit-test</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">@@ -2,12 +2,12 @@</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="shell"></span>
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="shell"><span class="nv" style="color: #008080;">pkg</span><span class="o" style="font-weight: 600;">=</span>picard-tools</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="shell"></span>
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5
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<pre style="margin: 0;">-<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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6
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<pre style="margin: 0;">-<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">DT</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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7
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<pre style="margin: 0;">-<span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="shell"><span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">[</span> <span class="s2" style="color: #d14;">"</span><span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="s2" style="color: #d14;">"</span> <span class="o" style="font-weight: 600;">=</span> <span class="s2" style="color: #d14;">""</span> <span class="o" style="font-weight: 600;">]</span> <span class="p">;</span> <span class="k" style="font-weight: 600;">then</span></span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="shell"><span class="k" style="font-weight: 600;"> </span><span class="nv" style="color: #008080;">A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="o" style="font-weight: 600;">=</span><span class="si" style="color: #d14;">$(</span><span class="nb" style="color: #0086b3;">mktemp</span> <span class="nt" style="color: #000080;">-d</span> /tmp/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span><span class="nt" style="color: #000080;">-test</span>.XXXXXX<span class="si" style="color: #d14;">)</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="shell"> <span class="nb" style="color: #0086b3;">trap</span> <span class="s2" style="color: #d14;">"rm -rf </span><span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span><span class="s2" style="color: #d14;">"</span> 0 INT QUIT ABRT PIPE TERM</span>
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8
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<pre style="margin: 0;"> <span id="LC8" class="line" lang="shell"><span class="k" style="font-weight: 600;">fi</span></span>
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="shell"></span>
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10
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<pre style="margin: 0;">-<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">DT</span>TMP</span></span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cd</span> <span class="nv" style="color: #008080;">$A<span class="idiff left right">UTOPKGTEST_</span>TMP</span></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">
11
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="shell"></span>
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12
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/unmapped.sam <span class="nb" style="color: #0086b3;">.</span></span>
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13
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="shell"><span class="nb" style="color: #0086b3;">cp</span> <span class="nt" style="color: #000080;">-a</span> /usr/share/doc/<span class="k" style="font-weight: 600;">${</span><span class="nv" style="color: #008080;">pkg</span><span class="k" style="font-weight: 600;">}</span>/test.<span class="k" style="font-weight: 600;">*</span> <span class="nb" style="color: #0086b3;">.</span></span>
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