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commit 7288af41e79fcbfa805f1771c7858c865a361e03 Author: Vincent Danjean <[email protected]> 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 <[email protected]> + 2013 Olivier Sallou <[email protected]> + 2015-2016 Vincent Danjean <[email protected]> +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 <[email protected]> - 2013 Olivier Sallou <[email protected]> - 2015 Vincent Danjean <[email protected]> -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. -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/picard-tools.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
