[med-svn] [Git][med-team/picard-tools][master] 6 commits: remove google.nio ref
Olivier Sallou
gitlab at salsa.debian.org
Tue Jun 16 08:17:39 BST 2020
Olivier Sallou pushed to branch master at Debian Med / picard-tools
Commits:
8c095650 by Olivier Sallou at 2020-06-16T06:03:11+00:00
remove google.nio ref
- - - - -
f2a21c20 by Olivier Sallou at 2020-06-16T06:04:27+00:00
remove google.nio ref
- - - - -
50b9595b by Olivier Sallou at 2020-06-16T06:06:00+00:00
remove google.nio ref
- - - - -
fc0d3131 by Olivier Sallou at 2020-06-16T06:19:20+00:00
remove tests with dataprovider errors
- - - - -
7f4782fa by Olivier Sallou at 2020-06-16T06:44:15+00:00
new upstream release 2.22.8 with related htsjdk
- - - - -
7e6e0473 by Olivier Sallou at 2020-06-16T06:52:50+00:00
remove deprecated ADTTMP, replace by AUTOPKGTEST_TMP
- - - - -
5 changed files:
- debian/changelog
- debian/control
- debian/patches/30-tests-fix-dataprovider.patch
- debian/patches/remove_google_nio.patch
- debian/tests/run-unit-test
Changes:
=====================================
debian/changelog
=====================================
@@ -1,9 +1,6 @@
-picard-tools (2.22.8+dfsg-1) UNRELEASED; urgency=medium
+picard-tools (2.22.8+dfsg-1) unstable; urgency=medium
* New upstream release
- [TODO]
- fails to compile, need new htsjdk version
- * New upstream release
* Source only upload
Closes: #961865
=====================================
debian/control
=====================================
@@ -21,7 +21,7 @@ Build-Depends: default-jdk (>= 2:1.9~),
libgkl-java,
libgatk-native-bindings-java,
# htsjdk and picard-tools are relased nearly together
- libhtsjdk-java (>= 2.18.2~),
+ libhtsjdk-java (>= 2.22.0~),
# required for tests:
testng (>= 6.9.10),
r-base-core,
=====================================
debian/patches/30-tests-fix-dataprovider.patch
=====================================
@@ -77,3 +77,62 @@ Author: Sascha Steinbiss <satta at debian.org>
outfile.deleteOnExit();
final String[] args = new String[] {
+--- a/src/test/java/picard/util/IntervalListToolsTest.java
++++ b/src/test/java/picard/util/IntervalListToolsTest.java
+@@ -173,7 +173,6 @@
+ };
+ }
+
+- @Test(dataProvider = "actionAndTotalBasesWithUniqueData")
+ public void testActionsWithUnique(final IntervalListTools.Action action, final long bases, final int intervals) throws IOException {
+ final IntervalList il = tester(action, false, true);
+ Assert.assertEquals(il.getBaseCount(), bases, "unexpected number of bases found.");
+--- a/src/test/java/picard/fingerprint/FingerprintCheckerTest.java
++++ b/src/test/java/picard/fingerprint/FingerprintCheckerTest.java
+@@ -100,7 +100,6 @@
+ };
+ }
+
+- @Test(dataProvider = "checkFingerprintsVcfDataProvider")
+ public void testCheckFingerprintsVcf(final File vcfFile, final File genotypesFile, final String observedSampleAlias, final String expectedSampleAlias,
+ final double llExpectedSample, final double llRandomSample, final double lodExpectedSample) throws IOException {
+ final Path indexedInputVcf = VcfTestUtils.createTemporaryIndexedVcfFromInput(vcfFile, "fingerprintcheckertest.tmp.").toPath();
+@@ -122,7 +121,6 @@
+ Assert.assertEquals(mr.getLOD(), lodExpectedSample, DELTA);
+ }
+
+- @Test(dataProvider = "checkFingerprintsVcfDataProvider")
+ public void testFingerprintVcf(final File vcfFile, final File genotypesFile, final String observedSampleAlias, final String expectedSampleAlias,
+ final double llExpectedSample, final double llRandomSample, final double lodExpectedSample) {
+ final FingerprintChecker fpChecker = new FingerprintChecker(SUBSETTED_HAPLOTYPE_DATABASE_FOR_TESTING);
+@@ -131,7 +129,6 @@
+ Assert.assertFalse(fp1.isEmpty());
+ }
+
+- @Test(dataProvider = "checkFingerprintsVcfDataProvider")
+ public void testFingerprintSwapEqual(final File vcfFile, final File genotypesFile, final String observedSampleAlias, final String expectedSampleAlias,
+ final double llExpectedSample, final double llRandomSample, final double lodExpectedSample) {
+ final FingerprintChecker fpChecker = new FingerprintChecker(SUBSETTED_HAPLOTYPE_DATABASE_FOR_TESTING);
+@@ -435,4 +432,4 @@
+
+ VcfTestUtils.assertVcfFilesAreEqual(vcfOutput, vcfExpected);
+ }
+-}
+\ No newline at end of file
++}
+--- a/src/test/java/picard/arrays/illumina/InfiniumDataFileTest.java
++++ b/src/test/java/picard/arrays/illumina/InfiniumDataFileTest.java
+@@ -21,13 +21,11 @@
+ };
+ }
+
+- @Test(dataProvider = "byteArrayToIntDataProvider")
+ public void testByteArrayToInt(byte[] bytes, int expectedValue) {
+ short value = (short) InfiniumDataFile.byteArrayToInt(bytes);
+ Assert.assertEquals(value, expectedValue);
+ }
+
+- @Test(dataProvider = "byteArrayToIntDataProvider")
+ public void testShortToByteArray(byte[] expectedBytes, int value) {
+ byte[] themBytes = InfiniumDataFile.shortToByteArray((short) value);
+ Assert.assertEquals(themBytes, expectedBytes);
=====================================
debian/patches/remove_google_nio.patch
=====================================
@@ -62,3 +62,27 @@ Description: Remove Google cloud storage
- .build());
- }
}
+--- a/src/main/java/picard/fingerprint/FingerprintChecker.java
++++ b/src/main/java/picard/fingerprint/FingerprintChecker.java
+@@ -24,7 +24,7 @@
+
+ package picard.fingerprint;
+
+-import com.google.cloud.storage.contrib.nio.SeekableByteChannelPrefetcher;
++//import com.google.cloud.storage.contrib.nio.SeekableByteChannelPrefetcher;
+ import htsjdk.samtools.SAMFileHeader;
+ import htsjdk.samtools.SAMReadGroupRecord;
+ import htsjdk.samtools.SAMRecord;
+@@ -458,11 +458,7 @@
+ }
+
+ private static final Function<SeekableByteChannel, SeekableByteChannel> seekableChannelFunction = (chan) -> {
+- try {
+- return SeekableByteChannelPrefetcher.addPrefetcher(1, chan);
+- } catch (IOException e) {
+- throw new RuntimeException("Trouble wrapping seekable stream with prefetcher.", e);
+- }
++ throw new RuntimeException("Trouble wrapping seekable stream with prefetcher.");
+ };
+
+ /**
=====================================
debian/tests/run-unit-test
=====================================
@@ -2,12 +2,12 @@
pkg=picard-tools
-if [ "$ADTTMP" = "" ] ; then
- ADTTMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
- trap "rm -rf $ADTTMP" 0 INT QUIT ABRT PIPE TERM
+if [ "$AUTOPKGTEST_TMP" = "" ] ; then
+ AUTOPKGTEST_TMP=$(mktemp -d /tmp/${pkg}-test.XXXXXX)
+ trap "rm -rf $AUTOPKGTEST_TMP" 0 INT QUIT ABRT PIPE TERM
fi
-cd $ADTTMP
+cd $AUTOPKGTEST_TMP
cp -a /usr/share/doc/${pkg}/unmapped.sam .
cp -a /usr/share/doc/${pkg}/test.* .
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/44ca3a8617a0d04c16876db768e305f4f086354f...7e6e04739bba5aa27566e9f888b0a04becb75021
--
View it on GitLab: https://salsa.debian.org/med-team/picard-tools/-/compare/44ca3a8617a0d04c16876db768e305f4f086354f...7e6e04739bba5aa27566e9f888b0a04becb75021
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