[med-svn] [picard-tools] 06/08: Update copyright

Vincent Danjean vdanjean at debian.org
Thu Jul 7 10:00:00 UTC 2016 

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vdanjean pushed a commit to branch master
in repository picard-tools.

commit 7288af41e79fcbfa805f1771c7858c865a361e03
Author: Vincent Danjean <vdanjean at debian.org>
Date:   Thu Jul 7 11:23:45 2016 +0200

    Update copyright
    
    "cme update dpkg-copyright" helped a lot
---
 debian/copyright | 291 +++++++++++++++++++++++++++++++++++++++++++++++++++++--
 1 file changed, 281 insertions(+), 10 deletions(-)

diff --git a/debian/copyright b/debian/copyright
index 5a593ce..49b44ed 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -6,6 +6,264 @@ Files-Excluded: gradle/wrapper/gradle-wrapper.jar
 Files: *
 Copyright: © 2009–2014 The Broad Institute
 License: MIT
+
+Files: debian/*
+Copyright: 2010 Shaun Jackman <sjackman at debian.org>
+           2013 Olivier Sallou <osallou at debian.org>
+           2015-2016 Vincent Danjean <vdanjean at debian.org>
+License: ISC
+
+Files: etc/test/junit-noframes.xsl
+Copyright: 2001-2004, The Apache Software Foundation
+License: Apache-2.0
+
+Files: src/main/java/*
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/main/java/picard/Test.java
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/analysis/CollectWgsMetricsWithNonZeroCoverage.java
+Copyright: 2015, 2016, Nils Homer
+License: Expat
+
+Files: src/main/java/picard/analysis/artifacts/*
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/analysis/directed/CollectTargetedMetrics.java
+  src/main/java/picard/analysis/directed/CollectTargetedPcrMetrics.java
+  src/main/java/picard/analysis/directed/InsertSizeMetricsCollector.java
+  src/main/java/picard/analysis/directed/RnaSeqMetricsCollector.java
+  src/main/java/picard/analysis/directed/TargetedPcrMetrics.java
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/cmdline/CommandLineDefaults.java
+  src/main/java/picard/cmdline/CommandLineProgramGroup.java
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/cmdline/programgroups/*
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/fastq/*
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/fastq/BamToBfq.java
+  src/main/java/picard/fastq/BamToBfqWriter.java
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/main/java/picard/illumina/CheckIlluminaDirectory.java
+  src/main/java/picard/illumina/IlluminaLaneMetrics.java
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/illumina/parser/BclData.java
+  src/main/java/picard/illumina/parser/IlluminaMetricsCode.java
+  src/main/java/picard/illumina/parser/MultiTileBclFileUtil.java
+  src/main/java/picard/illumina/parser/MultiTileFileUtil.java
+  src/main/java/picard/illumina/parser/ParameterizedFileUtil.java
+  src/main/java/picard/illumina/parser/PerTileFileUtil.java
+  src/main/java/picard/illumina/parser/PerTilePerCycleFileUtil.java
+  src/main/java/picard/illumina/parser/TilePhasingValue.java
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/illumina/parser/fakers/*
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/illumina/parser/readers/BarcodeFileReader.java
+  src/main/java/picard/illumina/parser/readers/BclQualityEvaluationStrategy.java
+  src/main/java/picard/illumina/parser/readers/TileMetricsOutReader.java
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/metrics/*
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/metrics/GcBiasMetrics.java
+  src/main/java/picard/metrics/MultiLevelCollector.java
+  src/main/java/picard/metrics/PerUnitMetricCollector.java
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/main/java/picard/pedigree/*
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/reference/NormalizeFasta.java
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/sam/AddCommentsToBam.java
+  src/main/java/picard/sam/AddOrReplaceReadGroups.java
+  src/main/java/picard/sam/CalculateReadGroupChecksum.java
+  src/main/java/picard/sam/CheckTerminatorBlock.java
+  src/main/java/picard/sam/GatherBamFiles.java
+  src/main/java/picard/sam/RevertOriginalBaseQualitiesAndAddMateCigar.java
+  src/main/java/picard/sam/SamAlignmentMerger.java
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/sam/util/*
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/sam/util/PhysicalLocationShort.java
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/main/java/picard/util/AdapterPair.java
+  src/main/java/picard/util/AtomicIterator.java
+  src/main/java/picard/util/BaitDesigner.java
+  src/main/java/picard/util/BedToIntervalList.java
+  src/main/java/picard/util/CircularByteBuffer.java
+  src/main/java/picard/util/CsvInputParser.java
+  src/main/java/picard/util/DelimitedTextFileWithHeaderIterator.java
+  src/main/java/picard/util/FifoBuffer.java
+  src/main/java/picard/util/IntervalListScatterer.java
+  src/main/java/picard/util/IntervalListTools.java
+  src/main/java/picard/util/Iterators.java
+  src/main/java/picard/util/QuerySortedReadPairIteratorUtil.java
+  src/main/java/picard/util/ScatterIntervalsByNs.java
+  src/main/java/picard/util/UnsignedTypeUtil.java
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/java/picard/util/IntervalListToBed.java
+Copyright: 2016, Tim Fennell
+License: Expat
+
+Files: src/main/java/picard/vcf/ByIntervalListVariantContextIterator.java
+  src/main/java/picard/vcf/GatherVcfs.java
+  src/main/java/picard/vcf/GenotypeConcordanceContingencyMetrics.java
+  src/main/java/picard/vcf/GenotypeConcordanceCounts.java
+  src/main/java/picard/vcf/GenotypeConcordanceDetailMetrics.java
+  src/main/java/picard/vcf/GenotypeConcordanceStateCodes.java
+  src/main/java/picard/vcf/GenotypeConcordanceStates.java
+  src/main/java/picard/vcf/GenotypeConcordanceSummaryMetrics.java
+  src/main/java/picard/vcf/LiftoverVcf.java
+  src/main/java/picard/vcf/MakeSitesOnlyVcf.java
+  src/main/java/picard/vcf/SortVcf.java
+  src/main/java/picard/vcf/SplitVcfs.java
+  src/main/java/picard/vcf/VcfToIntervalList.java
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/main/resources/release_picard.sh
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/test/java/picard/analysis/CollectAlignmentSummaryMetricsTest.java
+  src/test/java/picard/analysis/CollectInsertSizeMetricsTest.java
+  src/test/java/picard/analysis/CollectQualityYieldMetricsTest.java
+  src/test/java/picard/analysis/CollectRnaSeqMetricsTest.java
+  src/test/java/picard/analysis/CollectWgsMetricsFromSampledSitesTest.java
+  src/test/java/picard/analysis/TheoreticalSensitivityTest.java
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/test/java/picard/cmdline/CommandLineParserTest.java
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/test/java/picard/fingerprint/HaplotypeMapTest.java
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java
+  src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java
+  src/test/java/picard/illumina/IlluminaBasecallsToSamAdapterClippingTest.java
+  src/test/java/picard/illumina/IlluminaBasecallsToSamTest.java
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/test/java/picard/illumina/parser/CycleIlluminaFileMapTest.java
+  src/test/java/picard/illumina/parser/IlluminaDataProviderTest.java
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/test/java/picard/illumina/parser/fakers/*
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/test/java/picard/metrics/*
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/test/java/picard/reference/*
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/test/java/picard/sam/*
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/test/java/picard/sam/AddCommentsToBamTest.java
+  src/test/java/picard/sam/GatherBamFilesTest.java
+  src/test/java/picard/sam/PositionBasedDownsampleSamTest.java
+  src/test/java/picard/sam/SetNmAndUqTagsTest.java
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/test/java/picard/sam/FilterSamReadsTest.java
+Copyright: © 2009–2014 The Broad Institute
+License: Expat
+
+Files: src/test/java/picard/sam/markduplicates/EstimateLibraryComplexityTest.java
+Copyright: 2015, 2016, Nils Homer
+License: Expat
+
+Files: src/test/java/picard/sam/markduplicates/MarkDuplicateWithMissingBarcodeTest.java
+  src/test/java/picard/sam/markduplicates/MarkDuplicateWithMissingReadOneBarcodeTest.java
+  src/test/java/picard/sam/markduplicates/MarkDuplicateWithMissingReadTwoBarcodeTest.java
+  src/test/java/picard/sam/markduplicates/MarkDuplicateWithMissingSampleBarcodeTest.java
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/test/java/picard/sam/markduplicates/util/*
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/test/java/picard/sam/testers/*
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/test/java/picard/sam/util/*
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+Files: src/test/java/picard/util/ClippingUtilityTest.java
+  src/test/java/picard/util/FileChannelJDKBugWorkAroundTest.java
+  src/test/java/picard/util/IntervalListScattererTest.java
+  src/test/java/picard/util/MergingIteratorTest.java
+  src/test/java/picard/util/RExecutorTest.java
+  src/test/java/picard/util/TextFileParsersTest.java
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/test/java/picard/vcf/*
+Copyright: 2009-2016, The Broad Institute
+License: Expat
+
+Files: src/test/java/picard/vcf/AbstractVcfMergingClpTester.java
+  src/test/java/picard/vcf/CallingMetricAccumulatorTest.java
+  src/test/java/picard/vcf/LiftoverVcfTest.java
+  src/test/java/picard/vcf/MergeVcfsTest.java
+  src/test/java/picard/vcf/SortVcfsTest.java
+  src/test/java/picard/vcf/SplitVcfsTest.java
+Copyright: © 2009–2014 The Broad Institute
+License: MIT
+
+License: MIT
  Permission is hereby granted, free of charge, to any person obtaining a copy
  of this software and associated documentation files (the "Software"), to deal
  in the Software without restriction, including without limitation the rights
@@ -24,8 +282,11 @@ License: MIT
  OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  THE SOFTWARE.
 
-Files: etc/test/junit-noframes.xsl
-Copyright: 2001-2004 The Apache Software Foundation
+License: ISC
+ Permission to use, copy, modify, and/or distribute this software for any
+ purpose with or without fee is hereby granted, provided that the above
+ copyright notice and this permission notice appear in all copies.
+
 License: Apache-2.0
  Licensed under the Apache License, Version 2.0 (the "License");
  you may not use this file except in compliance with the License.
@@ -41,11 +302,21 @@ License: Apache-2.0
 Comment: On Debian systems, the complete text of the Apache License version 2.0
  is available in the file ‘/usr/share/common-licenses/Apache-2.0’.
 
-Files: debian/*
-Copyright: 2010 Shaun Jackman <sjackman at debian.org>
-           2013 Olivier Sallou <osallou at debian.org>
-           2015 Vincent Danjean <vdanjean at debian.org>
-License: ISC
- Permission to use, copy, modify, and/or distribute this software for any
- purpose with or without fee is hereby granted, provided that the above
- copyright notice and this permission notice appear in all copies.
+License: Expat
+ Permission is hereby granted, free of charge, to any person obtaining a copy
+ of this software and associated documentation files (the "Software"), to deal
+ in the Software without restriction, including without limitation the rights
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ copies of the Software, and to permit persons to whom the Software is
+ furnished to do so, subject to the following conditions:
+ .
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
+ .
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+ THE SOFTWARE.

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