Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ Source: https://github.com/broadinstitute/picard/releases Comment: Convenience binary jar files are removed. Files-Excluded: gradle/wrapper/gradle-wrapper.jar *.bak Files: * Copyright: © 2009–2014 The Broad Institute License: MIT Files: debian/* Copyright: 2010 Shaun Jackman 2013 Olivier Sallou 2015-2016 Vincent Danjean 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 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 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. 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. You may obtain a copy of the License at . http://www.apache.org/licenses/LICENSE-2.0 . Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. 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’. 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.