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<h3>
Dylan Aïssi pushed to branch master
at <a href="https://salsa.debian.org/med-team/beagle">Debian Med / beagle</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/-/commit/699eed2975f501a3637ccee42d3c17f16acb3ae2">699eed29</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-05-31T15:59:56+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 5.1-200518+dfsg</pre>
</li>
<li>
<strong><a href="https://salsa.debian.org/med-team/beagle/-/commit/da7be15b68c23ba9b14ea4e086686f903b35f275">da7be15b</a></strong>
<div>
<span>by Dylan Aïssi</span>
<i>at 2020-05-31T15:59:57+02:00</i>
</div>
<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Update upstream source from tag 'upstream/5.1-200518+dfsg'
Update to upstream version '5.1-200518+dfsg'
with Debian dir 56567ebc98f963a4a03104de3a90c3db1358df09</pre>
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<h4>2 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#2ad0efaccf66628e1858a4c133e8914e33eb2221">
main/Main.java
</a>
</li>
<li class="file-stats">
<a href="#eb8feff2ab6118f4d6e39c9b23f9be1bb268f0f5">
vcf/BasicMarker.java
</a>
</li>
</ul>
<h4>Changes:</h4>
<li id="2ad0efaccf66628e1858a4c133e8914e33eb2221">
<a href="https://salsa.debian.org/med-team/beagle/-/compare/4c7f85fb460be2def9bb05ae998090e7eccfda41...da7be15b68c23ba9b14ea4e086686f903b35f275#2ad0efaccf66628e1858a4c133e8914e33eb2221"><strong>main/Main.java</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">@@ -65,8 +65,8 @@ public class Main {</td>
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<pre style="margin: 0;"> <span id="LC65" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The program name and version.</span></span>
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<pre style="margin: 0;"> <span id="LC66" 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="LC67" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">VERSION</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"(version 5.1)"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC68" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">PROGRAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"beagle.<span class="idiff left right">27Apr20.b81</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC69" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">COMMAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"java -jar beagle.<span class="idiff left right">27Apr20.b81</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">PROGRAM</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"beagle.<span class="idiff left right">18May20.d20</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">COMMAND</span> <span class="o" style="font-weight: 600;">=</span> <span class="s" style="color: #d14;">"java -jar beagle.<span class="idiff left right">18May20.d20</span>.jar"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC71" 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="LC72" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * The copyright string.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="78" 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="78" 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">@@ -78,7 +78,7 @@ public class Main {</td>
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<pre style="margin: 0;"> <span id="LC78" 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="LC79" class="line" lang="java"> <span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="no" style="color: #008080;">SHORT_HELP</span> <span class="o" style="font-weight: 600;">=</span> <span class="nc" style="color: #458; font-weight: 600;">Main</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">PROGRAM</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">" "</span> <span class="o" style="font-weight: 600;">+</span> <span class="no" style="color: #008080;">VERSION</span></span>
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<pre style="margin: 0;"> <span id="LC80" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Main</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">COPYRIGHT</span></span>
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<pre style="margin: 0;">-<span id="LC81" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Enter \"java -jar beagle.<span class="idiff left right">27Apr20.b81</span>.jar\" to "</span></span>
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="nc" style="color: #458; font-weight: 600;">Const</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">nl</span> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"Enter \"java -jar beagle.<span class="idiff left right">18May20.d20</span>.jar\" to "</span></span>
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<pre style="margin: 0;"> <span id="LC82" class="line" lang="java"> <span class="o" style="font-weight: 600;">+</span> <span class="s" style="color: #d14;">"list command line argument"</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC83" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC84" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Par</span> <span class="n" style="color: #333;">par</span><span class="o" style="font-weight: 600;">;</span></span>
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<li id="eb8feff2ab6118f4d6e39c9b23f9be1bb268f0f5">
<a href="https://salsa.debian.org/med-team/beagle/-/compare/4c7f85fb460be2def9bb05ae998090e7eccfda41...da7be15b68c23ba9b14ea4e086686f903b35f275#eb8feff2ab6118f4d6e39c9b23f9be1bb268f0f5"><strong>vcf/BasicMarker.java</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">@@ -23,10 +23,9 @@ import blbutil.Const;</td>
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<pre style="margin: 0;"> <span id="LC23" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">blbutil.StringUtil</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">blbutil.Utilities</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Arrays</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC26" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.HashMap</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.HashSet</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">-<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Map</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC27" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.Set</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="java"><span class="kn" style="font-weight: 600;">import</span> <span class="nn" style="color: #555;">java.util.concurrent.ConcurrentHashMap</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC29" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC30" 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="LC31" class="line" lang="java"><span class="cm" style="color: #998; font-style: italic;"> * <p>Class {@code BasicMarker} represents a genetic marker.</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="39" 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>
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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">@@ -39,8 +38,8 @@ import java.util.Set;</td>
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<pre style="margin: 0;"> <span id="LC38" class="line" lang="java"><span class="kd" style="font-weight: 600;">public</span> <span class="kd" style="font-weight: 600;">class</span> <span class="nc" style="color: #458; font-weight: 600;">BasicMarker</span> <span class="kd" style="font-weight: 600;">implements</span> <span class="nc" style="color: #458; font-weight: 600;">Marker</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC39" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC40" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="no" style="color: #008080;">EMPTY_ID_ARRAY</span> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">];</span></span>
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<pre style="margin: 0;">-<span id="LC42" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]></span> <span class="no" style="color: #008080;">ALLELES_MAP</span></span>
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<pre style="margin: 0;">-<span id="LC43" class="line" lang="java"> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">HashMap</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><>(</span></span><span class="mi" style="color: #099;"><span class="idiff">24</span></span><span class="o" style="font-weight: 600;"><span class="idiff right">);</span></span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left right">ConcurrentHash</span>Map</span><span class="o" style="font-weight: 600;"><</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">,</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]></span> <span class="no" style="color: #008080;">ALLELES_MAP</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="java"> <span class="o" style="font-weight: 600;">=</span> <span class="k" style="font-weight: 600;">new</span> <span class="nc" style="color: #458; font-weight: 600;"><span class="idiff left">ConcurrentHashMap</span></span><span class="o" style="font-weight: 600;"><span class="idiff"><>(</span></span><span class="mi" style="color: #099;"><span class="idiff">24</span></span><span class="o" style="font-weight: 600;"><span class="idiff">);</span></span><span class="idiff"> </span><span class="c1" style="color: #998; font-style: italic;"><span class="idiff right">// allows re-use of String[] arrays</span></span></span>
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<pre style="margin: 0;"> <span id="LC43" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC44" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</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;">chromIndex</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;"> <span id="LC45" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</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;">pos</span><span class="o" style="font-weight: 600;">;</span></span>
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<td class="diff-line-num unfold js-unfold old_line" data-linenumber="189" 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>
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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">@@ -189,7 +188,7 @@ public class BasicMarker implements Marker {</td>
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<pre style="margin: 0;"> <span id="LC188" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC189" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC190" class="line" lang="java"></span>
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<pre style="margin: 0;">-<span id="LC192" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/* Return specified String[] alleles if not a SNV */</span></span>
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="java"> <span class="cm" style="color: #998; font-style: italic;">/* Return<span class="idiff left right">s</span> specified String[] alleles if not a SNV */</span></span>
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<pre style="margin: 0;"> <span id="LC192" class="line" lang="java"> <span class="kd" style="font-weight: 600;">private</span> <span class="kd" style="font-weight: 600;">static</span> <span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="nf" style="color: #900; font-weight: 600;">canonicalAlleles</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">String</span><span class="o" style="font-weight: 600;">[]</span> <span class="n" style="color: #333;">alleles</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;"> <span id="LC193" 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;">isSNV</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">alleles</span><span class="o" style="font-weight: 600;">))</span> <span class="o" style="font-weight: 600;">{</span></span>
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195
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<pre style="margin: 0;"> <span id="LC194" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">String</span> <span class="n" style="color: #333;">key</span> <span class="o" style="font-weight: 600;">=</span> <span class="n" style="color: #333;">alleles</span><span class="o" style="font-weight: 600;">[</span><span class="mi" style="color: #099;">0</span><span class="o" style="font-weight: 600;">];</span></span>
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