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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>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/535978884c37e61d8560d81f1a45c2cf9dbf872c">53597888</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2019-01-25T08:00:14Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">use scala-library 2.11 (2.12 not in debian)
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/f8b2102c6a9683ded805cef5036e05fb0bb73882">f8b2102c</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2019-01-25T08:09:20Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">remove test failing due to testng version with reflection data provider issues
</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/htsjdk/commit/fc6971e58f3c0844ad23093039fee81b1eb0af64">fc6971e5</a></strong>
<div>
<span>by Olivier Sallou</span>
<i>at 2019-01-25T08:14:36Z</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">fix lint warn
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#9c96da0e9f91d7d8937b69b524702c106258f0d1">
debian/changelog
</a>
</li>
<li class="file-stats">
<a href="#1e654adf99a8c857b5731b0e3de199d955a3d7ca">
<span class="new-file">
+
debian/patches/110-debian-lib-version.patch
</span>
</a>
</li>
<li class="file-stats">
<a href="#1829ef4ce68fdf0343d52cba28050f16f50ac5d0">
debian/patches/70-removesometests-testng.patch
</a>
</li>
<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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</li>
</ul>
<h4>Changes:</h4>
<li id="9c96da0e9f91d7d8937b69b524702c106258f0d1">
<a href="https://salsa.debian.org/med-team/htsjdk/compare/3b36bbcfc8c0e131f5292530a2da483803aa9b88...fc6971e58f3c0844ad23093039fee81b1eb0af64#9c96da0e9f91d7d8937b69b524702c106258f0d1"><strong>debian/changelog</strong></a>
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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="LC1" class="line" lang="plaintext">htsjdk (2.18.2+dfsg-1) UNRELEASED; 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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<pre style="margin: 0;">-<span id="LC3" class="line" lang="plaintext"> TODO: Fix or drop failing tests</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"> * New upstream version</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"> * debhelper 12</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="LC5" class="line" lang="plaintext"> * Standards-Version: 4.3.0</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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<td class="line_content noteable_line" style="padding-left: 0.5em; padding-right: 0.5em;">
<pre style="margin: 0;"> <span id="LC6" class="line" lang="plaintext"> * Remove trailing whitespace in debian/changelog</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"></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="plaintext"> [ Olivier Sallou ]</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="plaintext"> * d/p/110-debian-lib-version.patch: use scala-library 2.11,</span>
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<td class="diff-line-num new new_line" data-linenumber="10" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="plaintext"> v2.12 not yet in Debian</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">
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="plaintext"> * fix some reflection tests issues with testng</span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="plaintext"></span>
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<td class="diff-line-num new_line" data-linenumber="13" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC13" class="line" lang="plaintext"> -- Andreas Tille <tille@debian.org> Thu, 24 Jan 2019 17:31:54 +0100</span>
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<pre style="margin: 0;"> <span id="LC14" class="line" lang="plaintext"></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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<td class="diff-line-num new_line" data-linenumber="15" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC15" class="line" lang="plaintext">htsjdk (2.16.1+dfsg-3) unstable; urgency=medium</span>
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<li id="1e654adf99a8c857b5731b0e3de199d955a3d7ca">
<a href="https://salsa.debian.org/med-team/htsjdk/compare/3b36bbcfc8c0e131f5292530a2da483803aa9b88...fc6971e58f3c0844ad23093039fee81b1eb0af64#1e654adf99a8c857b5731b0e3de199d955a3d7ca"><strong>debian/patches/110-debian-lib-version.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff">Subject: use debian available library version</span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff">Description: scala-library 2.12 not yet in debian, use 2.11</span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff">Author: Olivier Sallou <osallou@debian.org></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff">Forwarded: no</span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">Last-Updated: 2019-01-25</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/build.gradle</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/build.gradle</span></span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -24,7 +24,7 @@</span></span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> compile "gov.nih.nlm.ncbi:ngs-java:2.9.0"</span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> compile "javax.xml.bind:jaxb-api:debian"</span>
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11
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"> </span>
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12
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- testCompile "org.scala-lang:scala-library:2.12.x"</span></span>
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13
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ testCompile "org.scala-lang:scala-library:2.11.x"</span></span>
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14
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> //testCompile "org.scalatest:scalatest_2.12:3.0.5"</span>
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15
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> //testRuntime 'org.pegdown:pegdown:1.6.0' // Necessary for generating HTML reports with ScalaTest</span>
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16
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"> testCompile "org.testng:testng:debian"</span></pre>
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<br>
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<li id="1829ef4ce68fdf0343d52cba28050f16f50ac5d0">
<a href="https://salsa.debian.org/med-team/htsjdk/compare/3b36bbcfc8c0e131f5292530a2da483803aa9b88...fc6971e58f3c0844ad23093039fee81b1eb0af64#1829ef4ce68fdf0343d52cba28050f16f50ac5d0"><strong>debian/patches/70-removesometests-testng.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -27,7 +27,7 @@ Last-Updated: 2018-02-19</td>
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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;">@@ -1<span class="idiff left right">15,10 +115</span>,10 @@</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;">@@ -1<span class="idiff left right">32,10 +132</span>,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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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -92,3 +92,27 @@ Last-Updated: 2018-02-19</td>
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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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<pre style="margin: 0;"> <span id="LC94" 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="LC95" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/src/test/java/htsjdk/samtools/cram/io/LTF8Test.java</span></span>
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/src/test/java/htsjdk/samtools/cram/io/LTF8Test.java</span></span>
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"><span class="gu" style="color: #800080; font-weight: 600;">@@ -52,21 +52,6 @@</span></span>
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> };</span>
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> </span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- @Test(dataProvider = "predefined")</span></span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- public void testPredefined (long value, byte[] ltf8) throws IOException {</span></span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- try (ByteArrayOutputStream ltf8TestBAOS = new ByteArrayOutputStream()) {</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final int len = LTF8.writeUnsignedLTF8(value, ltf8TestBAOS);</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Assert.assertTrue(len <= LTF8.MAX_BITS);</span></span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- byte[] actualArray = ltf8TestBAOS.toByteArray();</span></span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Assert.assertEquals(ltf8, actualArray);</span></span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">-</span></span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- try (ByteArrayInputStream ltf8TestBAIS = new ByteArrayInputStream(actualArray)) {</span></span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- final long actual = LTF8.readUnsignedLTF8(ltf8TestBAIS);</span></span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- Assert.assertEquals(actual, value);</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- }</span></span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> </span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"> @Test(expectedExceptions = RuntimeEOFException.class)</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> public void emptyStreamTest() throws IOException {</span></pre>
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<a href="https://salsa.debian.org/med-team/htsjdk/compare/3b36bbcfc8c0e131f5292530a2da483803aa9b88...fc6971e58f3c0844ad23093039fee81b1eb0af64#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">@@ -10,3 +10,4 @@</td>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="plaintext">90-disable-testftp.patch</span>
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="plaintext">92-disable-testhttp.patch</span>
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<pre style="margin: 0;"> <span id="LC12" class="line" lang="plaintext">100-fix-java11</span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="plaintext">110-debian-lib-version.patch</span></pre>
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