[med-svn] [htsjdk] 07/10: Addapt patches
Andreas Tille
tille at debian.org
Wed Jun 29 12:18:44 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 a10cf9adb49fee8017c62a0da75762fce0fbd7ff
Author: Andreas Tille <tille at debian.org>
Date: Wed Jun 29 10:15:00 2016 +0200
Addapt patches
---
debian/patches/11-snappy-java-compatibility.patch | 4 +-
debian/patches/12-use_libjbzip2-java | 27 -------------
debian/patches/13-skip_network_tests | 47 ++++++++---------------
debian/patches/14-skip_local_zlib_tests | 28 --------------
debian/patches/series | 2 -
5 files changed, 17 insertions(+), 91 deletions(-)
diff --git a/debian/patches/11-snappy-java-compatibility.patch b/debian/patches/11-snappy-java-compatibility.patch
index 23fe89c..a74f720 100644
--- a/debian/patches/11-snappy-java-compatibility.patch
+++ b/debian/patches/11-snappy-java-compatibility.patch
@@ -3,8 +3,8 @@ Description: Fix the compatibility with the latest version of snappy-java.
(which is true in Debian).
Author: Emmanuel Bourg <ebourg at apache.org>
Forwarded: not-needed
---- a/src/java/htsjdk/samtools/util/SnappyLoader.java
-+++ b/src/java/htsjdk/samtools/util/SnappyLoader.java
+--- a/src/main/java/htsjdk/samtools/util/SnappyLoader.java
++++ b/src/main/java/htsjdk/samtools/util/SnappyLoader.java
@@ -24,7 +24,6 @@
package htsjdk.samtools.util;
diff --git a/debian/patches/12-use_libjbzip2-java b/debian/patches/12-use_libjbzip2-java
deleted file mode 100644
index 9d602e2..0000000
--- a/debian/patches/12-use_libjbzip2-java
+++ /dev/null
@@ -1,27 +0,0 @@
-Subject: use libjbzip2-java classes
-Description: Debian package for this class
- is libjbzip2-java, need to update package
- name
-Author: Olivier Sallou <osallou at debian.org>
-Last-Updated: 2012-08-31
-Forwarded: not-needed
---- a/src/java/htsjdk/samtools/cram/io/ExternalCompression.java
-+++ b/src/java/htsjdk/samtools/cram/io/ExternalCompression.java
-@@ -5,7 +5,7 @@ import htsjdk.samtools.util.IOUtil;
- import org.apache.commons.compress.compressors.bzip2.BZip2CompressorInputStream;
- import org.apache.commons.compress.compressors.xz.XZCompressorInputStream;
- import org.apache.commons.compress.compressors.xz.XZCompressorOutputStream;
--import org.apache.tools.bzip2.CBZip2InputStream;
-+import org.itadaki.bzip2.BZip2InputStream;
-
- import java.io.ByteArrayInputStream;
- import java.io.ByteArrayOutputStream;
-@@ -74,7 +74,7 @@ public class ExternalCompression {
- // hello, apache!
- byteArrayInputStream.read();
- byteArrayInputStream.read();
-- return InputStreamUtils.readFully(new CBZip2InputStream(byteArrayInputStream));
-+ return InputStreamUtils.readFully(new BZip2InputStream(byteArrayInputStream, false));
- }
-
- /**
diff --git a/debian/patches/13-skip_network_tests b/debian/patches/13-skip_network_tests
index bfc8647..2040700 100644
--- a/debian/patches/13-skip_network_tests
+++ b/debian/patches/13-skip_network_tests
@@ -3,8 +3,8 @@ Subject: disable network tests
Description: remove network related tests
fixing bug 808593
Last-Updated: 2015-01-06
---- a/src/tests/java/htsjdk/tribble/util/ParsingUtilsTest.java
-+++ b/src/tests/java/htsjdk/tribble/util/ParsingUtilsTest.java
+--- a/src/test/java/htsjdk/tribble/util/ParsingUtilsTest.java
++++ b/src/test/java/htsjdk/tribble/util/ParsingUtilsTest.java
@@ -117,47 +117,12 @@ public class ParsingUtilsTest {
testSplitJoinRoundtrip("\ta\tb", '\t', Arrays.asList("", "a", "b"));
}
@@ -53,8 +53,8 @@ Last-Updated: 2015-01-06
}
---- a/src/tests/java/htsjdk/tribble/AbstractFeatureReaderTest.java
-+++ b/src/tests/java/htsjdk/tribble/AbstractFeatureReaderTest.java
+--- a/src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java
++++ b/src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java
@@ -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";
@@ -142,11 +142,11 @@ Last-Updated: 2015-01-06
- }
-
}
---- a/src/tests/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
-+++ b/src/tests/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
+--- a/src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
++++ b/src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
@@ -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");
+ private static File TestFile = new File("src/test/resources/htsjdk/samtools/seekablestream/megabyteZeros.dat");
- /**
- * Test reading across a buffer boundary (buffer size is 512000). The test first reads a range of
@@ -203,8 +203,8 @@ Last-Updated: 2015-01-06
@Test
public void testSkip() throws IOException {
---- a/src/tests/java/htsjdk/samtools/sra/SRAIndexTest.java
-+++ b/src/tests/java/htsjdk/samtools/sra/SRAIndexTest.java
+--- a/src/test/java/htsjdk/samtools/sra/SRAIndexTest.java
++++ b/src/test/java/htsjdk/samtools/sra/SRAIndexTest.java
@@ -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];
@@ -291,34 +291,17 @@ Last-Updated: 2015-01-06
- return (SRAIndex) reader.getIndex();
- }
}
---- a/build.xml
-+++ b/build.xml
-@@ -151,6 +151,15 @@
- </classpath>
- <classfileset dir="${classes.test}">
- <include name="**/Test*.class"/>
-+ <exclude name="**/BAM*.class"/>
-+ <exclude name="**/CRAM*.class"/>
-+ <exclude name="**/SAM*.class"/>
-+ <exclude name="**/Sam*.class"/>
-+ <exclude name="**/Tabix*.class"/>
-+ <exclude name="**/SRA*.class"/>
-+ <exclude name="**/*FTP*.class"/>
-+ <exclude name="**/EnaRef*.class"/>
-+ <exclude name="**/IupacTest*.class"/>
- <include name="**/*Test.class"/>
- </classfileset>
- <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 @@ import java.util.TreeSet;
+--- a/src/test/java/htsjdk/samtools/sra/SRATest.java
++++ b/src/test/java/htsjdk/samtools/sra/SRATest.java
+@@ -57,376 +57,4 @@ import java.util.TreeSet;
*/
public class SRATest extends AbstractSRATest {
- @DataProvider(name = "testCounts")
- private Object[][] createDataForCounts() {
- return new Object[][] {
-- {"SRR2096940", 10591, 498}
+- {"SRR2096940", 10591, 498},
+- {"SRR000123", 0, 4583}
- };
- }
-
@@ -488,7 +471,7 @@ Last-Updated: 2015-01-06
- 1787186, "38M63S", "gi|169794206|ref|NC_010410.1|", 11, true, true},
-
- // local SRA file
-- {"testdata/htsjdk/samtools/sra/test_archive.sra", 1, 99, "test_archive.R.2",
+- {"src/test/resources/htsjdk/samtools/sra/test_archive.sra", 1, 99, "test_archive.R.2",
- "TGTCGATGCTGAAAGTGTCTGCGGTGAACCACTTCATGCACAGCGCACACTGCAGCTCCACTTCACCCAGCTGACGGCCGTTCTCATCGTCTCCAGAGCCCGTCTGAGCGTCCGCTGCTTCAGAACTGTCCCCGGCTGTATCCTGAAGAC",
- "BBAABBBFAFFFGGGGGGGGGGGGEEFHHHHGHHHHHFHHGHFDGGGGGHHGHHHHHHHHHHHHFHHHGHHHHHHGGGGGGGHGGHHHHHHHHHGHHHHHGGGGHGHHHGGGGGGGGGHHHHEHHHHHHHHHHGCGGGHHHHHHGBFFGF",
- 2811570, "150M", "NC_007121.5", 60, true, false}
diff --git a/debian/patches/14-skip_local_zlib_tests b/debian/patches/14-skip_local_zlib_tests
deleted file mode 100644
index e314bd6..0000000
--- a/debian/patches/14-skip_local_zlib_tests
+++ /dev/null
@@ -1,28 +0,0 @@
-Skip test for the use of the local zlib implementation
-
-The error in the tests seems to come from the (local) zip lib that is not used.
-The comments in src/java/htsjdk/samtools/util/zip/DeflaterFactory.java
-seems to show that
-- this is not a big issue (at most, it will be a little slower)
-- this is uneeded with JDK8 (and it seems we are using it now):
- "Note that this class will no longer be necessary once Java 8 is
- required, because[...]"
---- a/src/tests/java/htsjdk/samtools/util/IntelDeflaterTest.java
-+++ b/src/tests/java/htsjdk/samtools/util/IntelDeflaterTest.java
-@@ -86,9 +86,13 @@
- outputFile.deleteOnExit();
-
-
-- Assert.assertTrue(DeflaterFactory.usingIntelDeflater(), "IntelDeflater is not loaded.");
-- log.info("IntelDeflater is loaded");
--
-+ //Assert.assertTrue(DeflaterFactory.usingIntelDeflater(), "IntelDeflater is not loaded.");
-+ //log.info("IntelDeflater is loaded");
-+ if (DeflaterFactory.usingIntelDeflater()) {
-+ log.info("IntelDeflater is loaded");
-+ } else {
-+ log.info("IntelDeflater is not loaded.");
-+ }
-
- SamReaderFactory readerFactory = SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
- if (eagerlyDecode) {
diff --git a/debian/patches/series b/debian/patches/series
index 901749e..11f1a22 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,5 +1,3 @@
# 10-build.xml
11-snappy-java-compatibility.patch
-12-use_libjbzip2-java
13-skip_network_tests
-14-skip_local_zlib_tests
--
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