[med-svn] [htsjdk] 04/05: Refresh patches
Andreas Tille
tille at debian.org
Fri May 20 09:49:28 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository htsjdk.
commit cf41a4955c6e82ccf9febd40850a60fbb4c59490
Author: Andreas Tille <tille at debian.org>
Date: Fri May 20 11:42:41 2016 +0200
Refresh patches
---
debian/patches/10-build.xml | 15 ++++----
debian/patches/13-skip_network_tests | 72 ++++++++++++++++++++++++++++++++----
2 files changed, 71 insertions(+), 16 deletions(-)
diff --git a/debian/patches/10-build.xml b/debian/patches/10-build.xml
index f9e8f35..a378084 100644
--- a/debian/patches/10-build.xml
+++ b/debian/patches/10-build.xml
@@ -7,20 +7,19 @@ Origin: vendor
Forwarded: no
--- a/build.xml
+++ b/build.xml
-@@ -39,8 +39,10 @@
- <property name="javac.debug" value="true"/>
+@@ -41,7 +41,10 @@
<!-- Get GIT hash, if available, otherwise leave it blank. -->
--
+
- <property name="repository.revision" value=""/>
+ <!-- For Debian, do not use GIT hash (it would be the one from the
+ packaging repo), but use the "dfsg" string as sources are
+ repacked -->
+ <property name="repository.revision" value="dfsg"/>
- <property name="htsjdk-version" value="2.1.1"/>
+ <property name="htsjdk-version" value="2.3.0"/>
<property name="htsjdk-version-file" value="htsjdk.version.properties"/>
<property name="testng.verbosity" value="2"/>
-@@ -72,6 +74,12 @@
+@@ -76,6 +79,12 @@
<fileset dir="${lib}">
<include name="**/*.jar"/>
</fileset>
@@ -33,7 +32,7 @@ Forwarded: no
</path>
</target>
-@@ -132,6 +140,7 @@
+@@ -138,6 +147,7 @@
<pathelement path="${classes}"/>
<pathelement path="${classes.test}"/>
<pathelement path="${scripts}"/>
@@ -41,7 +40,7 @@ Forwarded: no
</classpath>
<classfileset dir="${classes.test}">
<include name="**/Test*.class"/>
-@@ -176,6 +185,7 @@
+@@ -188,6 +198,7 @@
<pathelement path="${classes}"/>
<pathelement path="${classes.test}"/>
<pathelement path="${scripts}"/>
@@ -49,7 +48,7 @@ Forwarded: no
</classpath>
<classfileset dir="${classes.test}">
<include name="**/${name}.class"/>
-@@ -218,8 +228,14 @@
+@@ -230,8 +241,14 @@
<fileset dir="${lib}">
<include name="**/*.jar" />
</fileset>
diff --git a/debian/patches/13-skip_network_tests b/debian/patches/13-skip_network_tests
index 8a7a562..bfc8647 100644
--- a/debian/patches/13-skip_network_tests
+++ b/debian/patches/13-skip_network_tests
@@ -5,7 +5,7 @@ Description: remove network related tests
Last-Updated: 2015-01-06
--- a/src/tests/java/htsjdk/tribble/util/ParsingUtilsTest.java
+++ b/src/tests/java/htsjdk/tribble/util/ParsingUtilsTest.java
-@@ -117,47 +117,12 @@
+@@ -117,47 +117,12 @@ public class ParsingUtilsTest {
testSplitJoinRoundtrip("\ta\tb", '\t', Arrays.asList("", "a", "b"));
}
@@ -55,7 +55,7 @@ Last-Updated: 2015-01-06
}
--- a/src/tests/java/htsjdk/tribble/AbstractFeatureReaderTest.java
+++ b/src/tests/java/htsjdk/tribble/AbstractFeatureReaderTest.java
-@@ -21,30 +21,5 @@
+@@ -26,86 +26,4 @@ public class AbstractFeatureReaderTest {
final static String HTTP_INDEXED_VCF_PATH = "http://www.broadinstitute.org/~picard/testdata/ex2.vcf";
final static String LOCAL_MIRROR_HTTP_INDEXED_VCF_PATH = VariantBaseTest.variantTestDataRoot + "ex2.vcf";
@@ -75,7 +75,7 @@ Last-Updated: 2015-01-06
- }
- assertFalse(localIterator.hasNext());
- }
-
+-
- @Test
- public void testLoadBEDFTP() throws Exception {
- final String path = "ftp://ftp.broadinstitute.org/distribution/igv/TEST/cpgIslands with spaces.hg18.bed";
@@ -85,10 +85,66 @@ Last-Updated: 2015-01-06
- assertNotNull(feat);
- }
- }
+-
+- @DataProvider(name = "blockCompressedExtensionExtensionStrings")
+- public Object[][] createBlockCompressedExtensionStrings() {
+- return new Object[][] {
+- { "testzip.gz", true },
+- { "test.gzip", true },
+- { "test.bgz", true },
+- { "test.bgzf", true },
+- { "test.bzip2", false }
+- };
+- }
+-
+- @Test(enabled = true, dataProvider = "blockCompressedExtensionExtensionStrings")
+- public void testBlockCompressionExtensionString(final String testString, final boolean expected) {
+- Assert.assertEquals(AbstractFeatureReader.hasBlockCompressedExtension(testString), expected);
+- }
+-
+- @Test(enabled = true, dataProvider = "blockCompressedExtensionExtensionStrings")
+- public void testBlockCompressionExtensionFile(final String testString, final boolean expected) {
+- Assert.assertEquals(AbstractFeatureReader.hasBlockCompressedExtension(new File(testString)), expected);
+- }
+-
+- @DataProvider(name = "blockCompressedExtensionExtensionURIStrings")
+- public Object[][] createBlockCompressedExtensionURIs() {
+- return new Object[][]{
+- {"testzip.gz", true},
+- {"test.gzip", true},
+- {"test.bgz", true},
+- {"test.bgzf", true},
+- {"test", false},
+- {"test.bzip2", false},
+-
+- {"https://www.googleapis.com/download/storage/v1/b/deflaux-public-test/o/NA12877.vcf.gz", true},
+- {"https://www.googleapis.com/download/storage/v1/b/deflaux-public-test/o/NA12877.vcf.gzip", true},
+- {"https://www.googleapis.com/download/storage/v1/b/deflaux-public-test/o/NA12877.vcf.bgz", true},
+- {"https://www.googleapis.com/download/storage/v1/b/deflaux-public-test/o/NA12877.vcf.bgzf", true},
+- {"https://www.googleapis.com/download/storage/v1/b/deflaux-public-test/o/NA12877.vcf.bzip2", false},
+- {"https://www.googleapis.com/download/storage/v1/b/deflaux-public-test/o/NA12877", false},
+-
+- {"https://www.googleapis.com/download/storage/v1/b/deflaux-public-test/o/NA12877.vcf.gz?alt=media", true},
+- {"https://www.googleapis.com/download/storage/v1/b/deflaux-public-test/o/NA12877.vcf.gzip?alt=media", true},
+- {"https://www.googleapis.com/download/storage/v1/b/deflaux-public-test/o/NA12877.vcf.bgz?alt=media", true},
+- {"https://www.googleapis.com/download/storage/v1/b/deflaux-public-test/o/NA12877.vcf.bgzf?alt=media", true},
+- {"https://www.googleapis.com/download/storage/v1/b/deflaux-public-test/o/NA12877.vcf.bzip2?alt=media", false},
+-
+- {"ftp://ftp.broadinstitute.org/distribution/igv/TEST/cpgIslands.hg18.gz", true},
+- {"ftp://ftp.broadinstitute.org/distribution/igv/TEST/cpgIslands.hg18.bed", false}
+- };
+- }
+-
+- @Test(enabled = true, dataProvider = "blockCompressedExtensionExtensionURIStrings")
+- public void testBlockCompressionExtension(final String testURIString, final boolean expected) throws URISyntaxException {
+- URI testURI = URI.create(testURIString);
+- Assert.assertEquals(AbstractFeatureReader.hasBlockCompressedExtension(testURI), expected);
+- }
+-
}
--- a/src/tests/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
+++ b/src/tests/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
-@@ -40,58 +40,7 @@
+@@ -40,58 +40,7 @@ public class SeekableBufferedStreamTest
private final String BAM_URL_STRING = "http://broadinstitute.github.io/picard/testdata/index_test.bam";
private static File TestFile = new File("testdata/htsjdk/samtools/seekablestream/megabyteZeros.dat");
@@ -149,7 +205,7 @@ Last-Updated: 2015-01-06
public void testSkip() throws IOException {
--- a/src/tests/java/htsjdk/samtools/sra/SRAIndexTest.java
+++ b/src/tests/java/htsjdk/samtools/sra/SRAIndexTest.java
-@@ -50,85 +50,4 @@
+@@ -50,85 +50,4 @@ public class SRAIndexTest extends Abstra
private static final int LAST_BIN_LEVEL = GenomicIndexUtil.LEVEL_STARTS.length - 1;
private static final int SRA_BIN_OFFSET = GenomicIndexUtil.LEVEL_STARTS[LAST_BIN_LEVEL];
@@ -237,7 +293,7 @@ Last-Updated: 2015-01-06
}
--- a/build.xml
+++ b/build.xml
-@@ -141,6 +141,15 @@
+@@ -151,6 +151,15 @@
</classpath>
<classfileset dir="${classes.test}">
<include name="**/Test*.class"/>
@@ -252,10 +308,10 @@ Last-Updated: 2015-01-06
+ <exclude name="**/IupacTest*.class"/>
<include name="**/*Test.class"/>
</classfileset>
- <jvmarg value="-Xmx2G"/>
+ <jvmarg line="-Xmx2G @{additionalJVMarg}"/>
--- a/src/tests/java/htsjdk/samtools/sra/SRATest.java
+++ b/src/tests/java/htsjdk/samtools/sra/SRATest.java
-@@ -57,375 +57,4 @@
+@@ -57,375 +57,4 @@ import java.util.TreeSet;
*/
public class SRATest extends AbstractSRATest {
--
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