picard-tools 2.8.1+dfsg-3 / usr / share / doc / picard-tools / copyright

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 <sjackman@debian.org>
           2013 Olivier Sallou <osallou@debian.org>
           2015-2016 Vincent Danjean <vdanjean@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
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
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 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.