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<h3>
Andreas Tille pushed to branch upstream
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/83ec790bdd93a561288ad0fc1230b3773777ad85">83ec790b</a></strong>
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<span>by Andreas Tille</span>
<i>at 2021-01-27T18:07:26+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.24.1+dfsg</pre>
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<h4>1 changed file:</h4>
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<a href="#31d5bba7653eec0636b3566e5f1e304222e78986">
src/main/java/picard/sam/HitsForInsert.java
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<h4>Changes:</h4>
<li id="31d5bba7653eec0636b3566e5f1e304222e78986">
<a href="https://salsa.debian.org/med-team/picard-tools/-/commit/83ec790bdd93a561288ad0fc1230b3773777ad85#31d5bba7653eec0636b3566e5f1e304222e78986"><strong>src/main/java/picard/sam/HitsForInsert.java</strong></a>
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<td class="diff-line-num unfold js-unfold new_line" data-linenumber="130" 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">@@ -130,7 +130,9 @@ class HitsForInsert {</td>
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<pre style="margin: 0;"> <span id="LC130" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> */</span></span>
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<pre style="margin: 0;"> <span id="LC131" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="nc" style="color: #458; font-weight: 600;">SAMRecord</span> <span class="nf" style="color: #900; font-weight: 600;">getFragment</span><span class="o" style="font-weight: 600;">(</span><span class="kd" style="font-weight: 600;">final</span> <span class="kt" style="color: #458; font-weight: 600;">int</span> <span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num old_line" data-linenumber="132" 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="132" 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="LC132" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">SAMRecord</span> <span class="n" style="color: #333;">samRecord</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">firstOfPairOrFragment</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">get</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">i</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num old old_line" data-linenumber="133" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #fac5cd; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#f9d7dc">
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<pre style="margin: 0;">-<span id="LC133" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">samRecord</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReadPairedFlag</span><span class="o" style="font-weight: 600;">())</span> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">UnsupportedOperationException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"getFragment called for paired read"</span><span class="o" style="font-weight: 600;">);</span></span>
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<td class="diff-line-num new new_line" data-linenumber="133" 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="LC133" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">samRecord</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getReadPairedFlag</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></span>
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<td class="diff-line-num new new_line" data-linenumber="134" 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="LC134" class="line" lang="java"> <span class="k" style="font-weight: 600;">throw</span> <span class="k" style="font-weight: 600;">new</span> <span class="nf" style="color: #900; font-weight: 600;">UnsupportedOperationException</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"getFragment called for paired read: "</span> <span class="o" style="font-weight: 600;">+</span> <span class="n" style="color: #333;">samRecord</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">toString</span><span class="o" style="font-weight: 600;">());</span></span>
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<td class="diff-line-num new new_line" data-linenumber="135" 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="LC135" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC136" class="line" lang="java"> <span class="k" style="font-weight: 600;">return</span> <span class="n" style="color: #333;">samRecord</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC137" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC138" class="line" lang="java"></span>
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