build.gradle | 169 33 + 136 - 0 !
1 file changed, 33 insertions(+), 136 deletions(-)

 modifies the upstream build system.

build.gradle | 21 1 + 20 - 0 !
1 file changed, 1 insertion(+), 20 deletions(-)

 do not use shadowjar

src/test/java/picard/analysis/directed/CollectHsMetricsTest.java | 36 18 + 18 - 0 !
src/test/java/picard/arrays/illumina/InfiniumDataFileTest.java | 2 0 + 2 - 0 !
src/test/java/picard/fingerprint/FingerprintCheckerTest.java | 5 1 + 4 - 0 !
src/test/java/picard/util/IntervalListToolsTest.java | 1 0 + 1 - 0 !
4 files changed, 19 insertions(+), 25 deletions(-)

 fix data provider requirements

build.gradle | 19 2 + 17 - 0 !
src/test/java/picard/analysis/TheoreticalSensitivityTest.java | 3 2 + 1 - 0 !
src/test/java/picard/analysis/artifacts/TransitionTest.java | 9 0 + 9 - 0 !
src/test/java/picard/analysis/directed/CollectHsMetricsTest.java | 50 1 + 49 - 0 !
src/test/java/picard/util/IntervalListToolsTest.java | 10 0 + 10 - 0 !
5 files changed, 5 insertions(+), 86 deletions(-)

 fix testng version and disable some tests.
 testng below or equal to 6.9.13.4 does not correctly map
 long and Integers. This leads to test issues when provider [0,9] values
 and methods expects a long (testng sends an Integer).
 This patch disable some tests around this

build.gradle | 9 9 + 0 - 0 !
src/main/java/picard/fingerprint/FingerprintChecker.java | 8 2 + 6 - 0 !
src/main/java/picard/nio/GoogleStorageUtils.java | 44 0 + 44 - 0 !
src/main/java/picard/nio/PicardBucketUtils.java | 19 1 + 18 - 0 !
src/test/java/picard/cmdline/CommandLineProgramTest.java | 6 0 + 6 - 0 !
src/test/java/picard/nio/PicardBucketUtilsTest.java | 5 1 + 4 - 0 !
src/test/java/picard/sam/CreateSequenceDictionaryTest.java | 37 0 + 37 - 0 !
src/test/java/picard/sam/RevertSamTest.java | 144 0 + 144 - 0 !
src/test/java/picard/util/IntervalListToolsTest.java | 77 2 + 75 - 0 !
9 files changed, 15 insertions(+), 334 deletions(-)

 remove google cloud storage

src/test/java/picard/illumina/ExtractIlluminaBarcodesTest.java | 27 0 + 27 - 0 !
src/test/java/picard/util/LiftoverVcfTest.java | 26 0 + 26 - 0 !
2 files changed, 53 deletions(-)

 some tests try to check that a non readable file or directory
 is correctly managed. However during Debian build, sometimes user is root
 and unreadable is not effective. This patch removes related tests
Last-Updated: 2019-01-18

src/test/java/picard/IntelInflaterDeflaterLoadTest.java | 4 4 + 0 - 0 !
1 file changed, 4 insertions(+)

 skip intel tests on non-intel

src/test/java/picard/util/IntervalListToolsTest.java | 12 6 + 6 - 0 !
1 file changed, 6 insertions(+), 6 deletions(-)

 providing test with the right data types as arguments
 Test testActionsWithDontMergeAbutting needs to be provided with
 three arguments, the second of which has type long. But the current data
 provider sends an int.

build.gradle | 7 7 + 0 - 0 !
1 file changed, 7 insertions(+)

 omitting the build of classes that use deprecated
 com.sun.javadoc package, which disappears in OpenJDK 17.

src/test/java/picard/sam/MergeBamAlignmentTest.java | 6 4 + 2 - 0 !
src/test/java/picard/vcf/UpdateVcfSequenceDictionaryTest.java | 5 3 + 2 - 0 !
2 files changed, 7 insertions(+), 4 deletions(-)

 according to
 https://docs.gradle.org/current/userguide/compatibility.html
 the version of Gradle we have in Debian currently does not support the default
 JDK, which is OpenJDK17. Until it does, some tests have to be deactivated as
 they cannot be provided with the --add-opens JVM args they need.

build.gradle | 2 2 + 0 - 0 !
src/test/java/picard/fastq/BamToBfqTest.java | 5 4 + 1 - 0 !
2 files changed, 6 insertions(+), 1 deletion(-)

 when switching from openjdk11 to openjdk17 in debian, one byte

src/test/java/picard/analysis/directed/CollectHsMetricsTest.java | 6 3 + 3 - 0 !
1 file changed, 3 insertions(+), 3 deletions(-)

 allowing for some delta in test, to avoid
 java.lang.AssertionError: expected [100000] but found [100000.0]
	at org.testng.Assert.fail(Assert.java:94)
	at org.testng.Assert.failNotEquals(Assert.java:513)
	at org.testng.Assert.assertEqualsImpl(Assert.java:135)
	at org.testng.Assert.assertEquals(Assert.java:116)
	at org.testng.Assert.assertEquals(Assert.java:179)
	at picard.analysis.directed.CollectHsMetricsTest.testHsMetricsF80DoesNotUseCovCap(CollectHsMetricsTest.java:202)

src/test/java/picard/nio/HttpNioIntegrationTest.java | 2 1 + 1 - 0 !
1 file changed, 1 insertion(+), 1 deletion(-)

 disabling tests requiring the network