debian/changelog

-picard-tools (2.18.14+dfsg-1) UNRELEASED; urgency=medium
+picard-tools (2.18.14+dfsg-1) unstable; urgency=medium
 
   * New upstream version
   * Standards-Version: 4.2.1
   * Fix link
     Closes: #905706
+  * Versioned Build-Depends: libhtsjdk-java (>= 2.16.1~)
+  * d/rules: Respect DEB_BUILD_OPTIONS in override_dh_auto_test
+  * Simplified d/copyright by not mentioning every single file
 
- -- Andreas Tille <tille@debian.org>  Mon, 17 Sep 2018 15:13:19 +0200
+ -- Andreas Tille <tille@debian.org>  Wed, 19 Sep 2018 09:20:48 +0200
 
 picard-tools (2.18.2+dfsg-1) unstable; urgency=medium
 

debian/control

@@ -19,7 +19,7 @@ Build-Depends: default-jdk (>= 2:1.9~),
                libgkl-java,
                libgatk-native-bindings-java,
 # htsjdk and picard-tools are relased nearly together
-               libhtsjdk-java (>= 2.14~),
+               libhtsjdk-java (>= 2.16.1~),
 # required for tests:
                testng (>= 6.9.10),
                r-base-core,

debian/copyright

@@ -5,283 +5,28 @@ Files-Excluded: gradle/wrapper/gradle-wrapper.jar
                 *.bak
 
 Files: *
-Copyright: © 2009–2014 The Broad Institute
-License: MIT
+Copyright: © 2009-2018 The Broad Institute
+License: Expat
 
 Files: debian/*
 Copyright: 2010 Shaun Jackman <sjackman@debian.org>
-           2013 Olivier Sallou <osallou@debian.org>
+           2013-2018 Olivier Sallou <osallou@debian.org>
            2015-2016 Vincent Danjean <vdanjean@debian.org>
+           2016-2018 Andreas Tille <tille@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

debian/patches/remove_failing_tests

---- a/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java
-+++ b/src/test/java/picard/illumina/IlluminaBasecallsToFastqTest.java
-@@ -140,10 +140,6 @@
-         runStandardTest(1, "dualBarcode.", "barcode_double.params", 2, "25T8B8B25T", DUAL_BASECALLS_DIR, DUAL_TEST_DATA_DIR);
-     }
- 
--    @Test
--    public void testCbclConvert() throws Exception {
--        runStandardTest(1, "dualBarcode.", "barcode_double.params", 2, "151T8B8B151T", TEST_DATA_DIR_WITH_CBCLS, DUAL_CBCL_TEST_DATA_DIR);
--    }
- 
-     @Test
-     public void testHiseqxSingleLocs() throws Exception {

debian/patches/remove_google_nio.patch

+Author: Olivier Sallou
+Last-Update: 2018-04-23 14:51:06
+Description: Remove Google cloud storage
+
 --- a/src/main/java/picard/nio/GoogleStorageUtils.java
 +++ b/src/main/java/picard/nio/GoogleStorageUtils.java
 @@ -24,12 +24,6 @@

debian/rules

@@ -17,10 +17,12 @@ override_dh_auto_build:
 	dh_auto_build -- jar javadoc
 
 override_dh_auto_test:
+ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
 	# Tests do not work with locales with a different decimal separator
 	# (for example ',') 
 	env LC_ALL=C \
 	dh_auto_build -- test
+endif
 
 override_dh_clean:
 	dh_clean

debian/tests/run-unit-test

@@ -14,6 +14,8 @@ cp -a /usr/share/doc/${pkg}/test.* .
 cp -a /usr/share/doc/${pkg}/mini.vcf* .
 gunzip -r *
 
+set -x
+
 PicardCommandLine ViewSam INPUT=unmapped.sam
 
 PicardCommandLine CollectSequencingArtifactMetrics I=test.sam O=test R=test.fasta