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Loading source files for package picard.metrics...
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Constructing Javadoc information...
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[loading /root/.gradle/caches/modules-2/files-2.1/com.github.samtools/htsjdk/4.2.0/7f2d3ae32888aacef94548c120142cb7f44b60fe/htsjdk-4.2.0.jar(/htsjdk/samtools/util/IntervalListReferenceSequenceMask.class)]
[loading /root/.gradle/caches/modules-2/files-2.1/com.github.samtools/htsjdk/4.2.0/7f2d3ae32888aacef94548c120142cb7f44b60fe/htsjdk-4.2.0.jar(/htsjdk/variant/variantcontext/VariantContext.class)]
[loading /root/.gradle/caches/modules-2/files-2.1/com.github.samtools/htsjdk/4.2.0/7f2d3ae32888aac13:18:07.851 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.analysis.CollectQualityYieldMetricsSNVQ.QualityYieldMetrics
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13:18:07.869 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.analysis.CollectOxoGMetrics.CpcgMetrics
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13:18:07.873 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.analysis.JumpingLibraryMetrics
13:18:07.873 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.analysis.FingerprintingSummaryMetrics
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13:18:07.876 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
13:18:07.877 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.analysis.CollectQualityYieldMetrics.QualityYieldMetrics
13:18:07.877 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.analysis.CollectQualityYieldMetricsFlow.QualityYieldMetricsFlow
13:18:07.878 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.analysis.CollectQualityYieldMetricsFlow.QualityYieldMetricsFlow
13:18:07.879 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.analysis.FingerprintingDetailMetrics
13:18:07.879 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
13:18:07.880 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.analysis.CollectRawWgsMetrics.RawWgsMetrics
13:18:07.881 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.analysis.GcBiasDetailMetrics
13:18:07.881 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
13:18:07.882 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.analysis.CollectWgsMetricsWithNonZeroCoverage.WgsMetricsWithNonZeroCoverage
13:18:07.887 WARN DefaultDocWorkUnitHandler - No group summary declared for: picard.metrics.GcBiasMetrics
ef94548c120142cb7f44b60fe/htsjdk-4.2.0.jar(/htsjdk/variant/vcf/VCFFileReader.class)]
[loading src/main/java/picard/vcf/ByIntervalListVariantContextIterator.java]
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[loading /root/.gradle/caches/modules-2/files-2.1/com.github.samtools/htsjdk/4.2.0/7f2d3ae32888aacef94548c120142cb7f44b60fe/htsjdk-4.2.0.jar(/htsjdk/samtools/DuplicateScoringStrategy$ScoringStrategy.class)]
[loading /root/.gradle/caches/modules-2/files-2.1/com.github.samtools/htsjdk/4.2.0/7f2d3ae32888aacef94548c120142cb7f44b60fe/htsjdk-4.2.0.jar(/htsjdk/samtools/MergingSamRecordIterator.class)]
[loading /root/.gradle/caches/modules-2/files-2.1/com.github.samtools/htsjdk/4.2.0/7f2d3ae32888aacef94548c120142cb7f44b60fe/htsjdk-4.2.0.jar(/htsjdk/samtools/SamFileHeaderMerger.class)]
[loading /root/.gradle/caches/modules-2/files-2.1/com.github.samtools/htsjdk/4.2.0/7f2d3ae32888aacef94548c120142cb7f44b60fe/htsjdk-4.2.0.jar(/htsjdk/samtools/SamInputResource.class)]
[loading src/main/java/picard/sam/DuplicationMetricsFactory.java]
[parsing started DirectoryFileObject[src/main/java:picard/sam/DuplicationMetricsFactory.java]]
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[loading src/main/java/picard/sam/markduplicates/MarkDuplicatesForFlowHelper.java]
[parsing started DirectoryFileObject[src/main/java:picard/sam/markduplicates/MarkDuplicatesForFlowHelper.java]]
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[loading src/main/java/picard/sam/util/PGTagArgumentCollection.java]
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[loading src/main/java/picard/sam/markduplicates/util/AbstractOpticalDuplicateFinderCommandLineProgram.java]
[parsing started DirectoryFileObject[src/main/java:picard/sam/markduplicates/util/AbstractOpticalDuplicateFinderCommandLineProgram.java]]
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[loading src/main/java/picard/sam/markduplicates/util/LibraryIdGenerator.java]
[parsing started DirectoryFileObject[src/main/java:picard/sam/markduplicates/util/LibraryIdGenerator.java]]
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[loading src/main/java/picard/sam/markduplicates/util/ReadEnds.java]
[parsing started DirectoryFileObject[src/main/java:picard/sam/markduplicates/util/ReadEnds.java]]
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[loading src/main/java/picard/sam/util/PhysicalLocationShort.java]
[parsing started DirectoryFileObject[src/main/java:picard/sam/util/PhysicalLocationShort.java]]
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[loading src/main/java/picard/sam/util/PhysicalLocationInt.java]
[parsing started DirectoryFileObject[src/main/java:picard/sam/util/PhysicalLocationInt.java]]
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[loading src/main/java/picard/sam/util/PhysicalLocation.java]
[parsing started DirectoryFileObject[src/main/java:picard/sam/util/PhysicalLocation.java]]
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[loading src/main/java/picard/sam/markduplicates/util/OpticalDuplicateFinder.java]
[parsing started DirectoryFileObject[src/main/java:picard/sam/markduplicates/util/OpticalDuplicateFinder.java]]
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[loading src/main/java/picard/sam/util/ReadNameParser.java]
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[loading src/main/java/picard/util/GraphUtils.java]
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