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<h3>
Steffen Möller 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/03adfbf4c97adb5d97508cbbbd4e51af9f00d1b3">03adfbf4</a></strong>
<div>
<span>by Steffen Moeller</span>
<i>at 2020-11-14T17:49:30+01:00</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">New upstream version 2.23.8+dfsg</pre>
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<h4>1 changed file:</h4>
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<li class="file-stats">
<a href="#3a02115cc24686ccecd94ec7f340c5890a553d38">
src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.java
</a>
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<h4>Changes:</h4>
<li id="3a02115cc24686ccecd94ec7f340c5890a553d38">
<a href="https://salsa.debian.org/med-team/picard-tools/-/commit/03adfbf4c97adb5d97508cbbbd4e51af9f00d1b3#3a02115cc24686ccecd94ec7f340c5890a553d38"><strong>src/main/java/picard/analysis/CollectAlignmentSummaryMetrics.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">@@ -140,14 +140,12 @@ public class CollectAlignmentSummaryMetrics extends SinglePassSamProgram {</td>
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<pre style="margin: 0;"> <span id="LC140" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IOUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">assertFileIsWritable</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">OUTPUT</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC141" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">HISTOGRAM_FILE</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</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="LC142" class="line" lang="java"> <span class="k" style="font-weight: 600;">if</span> <span class="o" style="font-weight: 600;">(!</span><span class="no" style="color: #008080;">METRIC_ACCUMULATION_LEVEL</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">contains</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">MetricAccumulationLevel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ALL_READS</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="LC143" class="line" lang="java"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">warn</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ReadLength histogram is calculated on all reads only, but ALL_READS were not "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">-<span id="LC144" class="line" lang="java"> <span class="s" style="color: #d14;">"included in the Metric Accumulation Levels. Adding ALL_READS so that you get the output you asked for."</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">-<span id="LC145" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// This tools is called from "Collect Multiple Metrics" and so changing the METRIC_ACCUMULATION_LEVEL directly can</span></span>
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<pre style="margin: 0;">-<span id="LC146" class="line" lang="java"> <span class="c1" style="color: #998; font-style: italic;">// have unintended consequences....only changing it for this tool.</span></span>
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<pre style="margin: 0;">-<span id="LC147" class="line" lang="java"> <span class="no" style="color: #008080;">METRIC_ACCUMULATION_LEVEL</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;">HashSet</span><span class="o" style="font-weight: 600;"><>(</span><span class="no" style="color: #008080;">METRIC_ACCUMULATION_LEVEL</span><span class="o" style="font-weight: 600;">);</span></span>
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148
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<pre style="margin: 0;">-<span id="LC148" class="line" lang="java"> <span class="no" style="color: #008080;">METRIC_ACCUMULATION_LEVEL</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">add</span><span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">MetricAccumulationLevel</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">ALL_READS</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="java"> <span class="n" style="color: #333;">log</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">error</span><span class="o" style="font-weight: 600;">(</span><span class="s" style="color: #d14;">"ReadLength histogram is calculated on all reads only, but ALL_READS were not "</span> <span class="o" style="font-weight: 600;">+</span></span>
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="java"> <span class="s" style="color: #d14;">"included in the Metric Accumulation Levels. Histogram will not be generated."</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="java"> <span class="no" style="color: #008080;">HISTOGRAM_FILE</span><span class="o" style="font-weight: 600;">=</span><span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">;</span></span>
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span> <span class="k" style="font-weight: 600;">else</span> <span class="o" style="font-weight: 600;">{</span></span>
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IOUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">assertFileIsWritable</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">HISTOGRAM_FILE</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC148" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;">-<span id="LC150" class="line" lang="java"> <span class="nc" style="color: #458; font-weight: 600;">IOUtil</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">assertFileIsWritable</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">HISTOGRAM_FILE</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC149" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC150" class="line" lang="java"></span>
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<pre style="margin: 0;"> <span id="LC151" 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;">header</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getSequenceDictionary</span><span class="o" style="font-weight: 600;">().</span><span class="na" style="color: #008080;">isEmpty</span><span class="o" style="font-weight: 600;">())</span> <span class="o" style="font-weight: 600;">{</span></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">@@ -176,10 +174,12 @@ public class CollectAlignmentSummaryMetrics extends SinglePassSamProgram {</td>
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174
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<pre style="margin: 0;"> <span id="LC174" class="line" lang="java"> <span class="kd" style="font-weight: 600;">final</span> <span class="nc" style="color: #458; font-weight: 600;">AlignmentSummaryMetricsCollector</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">GroupAlignmentSummaryMetricsPerUnitMetricCollector</span> <span class="n" style="color: #333;">allReadsGroupCollector</span> <span class="o" style="font-weight: 600;">=</span></span>
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177
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<pre style="margin: 0;"> <span id="LC175" class="line" lang="java"> <span class="o" style="font-weight: 600;">(</span><span class="nc" style="color: #458; font-weight: 600;">AlignmentSummaryMetricsCollector</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">GroupAlignmentSummaryMetricsPerUnitMetricCollector</span><span class="o" style="font-weight: 600;">)</span> <span class="n" style="color: #333;">collector</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">getAllReadsCollector</span><span class="o" style="font-weight: 600;">();</span></span>
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178
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176
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<pre style="margin: 0;"> <span id="LC176" class="line" lang="java"></span>
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179
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<pre style="margin: 0;">-<span id="LC179" class="line" lang="java"> <span class="n" style="color: #333;">addAllHistogramToMetrics</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"PAIRED_TOTAL_LENGTH_COUNT"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">allReadsGroupCollector</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pairCollector</span><span class="o" style="font-weight: 600;">);</span></span>
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180
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<pre style="margin: 0;">-<span id="LC180" class="line" lang="java"> <span class="n" style="color: #333;">addAlignedHistogramToMetrics</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"PAIRED_ALIGNED_LENGTH_COUNT"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">allReadsGroupCollector</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pairCollector</span><span class="o" style="font-weight: 600;">);</span></span>
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181
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<pre style="margin: 0;">-<span id="LC181" class="line" lang="java"> <span class="n" style="color: #333;">addAllHistogramToMetrics</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"UNPAIRED_TOTAL_LENGTH_COUNT"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">allReadsGroupCollector</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">unpairedCollector</span><span class="o" style="font-weight: 600;">);</span></span>
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182
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<pre style="margin: 0;">-<span id="LC182" class="line" lang="java"> <span class="n" style="color: #333;">addAlignedHistogramToMetrics</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"UNPAIRED_ALIGNED_LENGTH_COUNT"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">allReadsGroupCollector</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">unpairedCollector</span><span class="o" style="font-weight: 600;">);</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" 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;">allReadsGroupCollector</span> <span class="o" style="font-weight: 600;">!=</span> <span class="kc" style="font-weight: 600;">null</span><span class="o" style="font-weight: 600;">)</span> <span class="o" style="font-weight: 600;">{</span></span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="java"> <span class="n" style="color: #333;">addAllHistogramToMetrics</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"PAIRED_TOTAL_LENGTH_COUNT"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">allReadsGroupCollector</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pairCollector</span><span class="o" style="font-weight: 600;">);</span></span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="java"> <span class="n" style="color: #333;">addAlignedHistogramToMetrics</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"PAIRED_ALIGNED_LENGTH_COUNT"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">allReadsGroupCollector</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">pairCollector</span><span class="o" style="font-weight: 600;">);</span></span>
</pre>
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="java"> <span class="n" style="color: #333;">addAllHistogramToMetrics</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"UNPAIRED_TOTAL_LENGTH_COUNT"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">allReadsGroupCollector</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">unpairedCollector</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="java"> <span class="n" style="color: #333;">addAlignedHistogramToMetrics</span><span class="o" style="font-weight: 600;">(</span><span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">,</span> <span class="s" style="color: #d14;">"UNPAIRED_ALIGNED_LENGTH_COUNT"</span><span class="o" style="font-weight: 600;">,</span> <span class="n" style="color: #333;">allReadsGroupCollector</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">unpairedCollector</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="java"> <span class="o" style="font-weight: 600;">}</span></span>
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<pre style="margin: 0;"> <span id="LC183" class="line" lang="java"></span>
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184
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<pre style="margin: 0;"> <span id="LC184" class="line" lang="java"> <span class="n" style="color: #333;">file</span><span class="o" style="font-weight: 600;">.</span><span class="na" style="color: #008080;">write</span><span class="o" style="font-weight: 600;">(</span><span class="no" style="color: #008080;">OUTPUT</span><span class="o" style="font-weight: 600;">);</span></span>
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<pre style="margin: 0;"> <span id="LC185" class="line" lang="java"></span>
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