[med-svn] [Git][med-team/picard-tools][master] 7 commits: Easier debugging fo tests
Andreas Tille
gitlab at salsa.debian.org
Wed Sep 19 09:39:00 BST 2018
Andreas Tille pushed to branch master at Debian Med / picard-tools
Commits:
9ee72387 by Andreas Tille at 2018-09-18T09:33:09Z
Easier debugging fo tests
- - - - -
84c4f9fb by Andreas Tille at 2018-09-19T06:43:58Z
Versioned Build-Depends: libhtsjdk-java (>= 2.16.1~)
- - - - -
e1206b5b by Andreas Tille at 2018-09-19T07:09:41Z
Add DEP3 description
- - - - -
0fd39c9a by Andreas Tille at 2018-09-19T07:10:14Z
Remove unused patch file
- - - - -
42dd97a6 by Andreas Tille at 2018-09-19T07:11:26Z
Respect DEB_BUILD_OPTIONS in override_dh_auto_test
- - - - -
19b4bb4c by Andreas Tille at 2018-09-19T07:20:31Z
Simplified d/copyright by not mentioning every single file which is not maintainable
- - - - -
598a6c68 by Andreas Tille at 2018-09-19T07:45:24Z
Upload to unstable
- - - - -
7 changed files:
- debian/changelog
- debian/control
- debian/copyright
- − debian/patches/remove_failing_tests
- debian/patches/remove_google_nio.patch
- debian/rules
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,11 +1,14 @@
-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 at debian.org> Mon, 17 Sep 2018 15:13:19 +0200
+ -- Andreas Tille <tille at 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 at debian.org>
- 2013 Olivier Sallou <osallou at debian.org>
+ 2013-2018 Olivier Sallou <osallou at debian.org>
2015-2016 Vincent Danjean <vdanjean at debian.org>
+ 2016-2018 Andreas Tille <tille 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
-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 deleted
=====================================
@@ -1,13 +0,0 @@
---- 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
=====================================
@@ -1,3 +1,7 @@
+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
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/ebd5740983b6575e0977672a2412d1497abef3cd...598a6c68b0ac62f69ff8221572311c08f66d683f
--
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/compare/ebd5740983b6575e0977672a2412d1497abef3cd...598a6c68b0ac62f69ff8221572311c08f66d683f
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