[med-svn] [htsjdk] 05/05: Adapt patches to new upstream version
Andreas Tille
tille at debian.org
Wed Oct 11 09:13:37 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository htsjdk.
commit 6494438fcb7c08a8f132885c5e9975a66c1f2cf0
Author: Andreas Tille <tille at debian.org>
Date: Wed Oct 11 10:32:05 2017 +0200
Adapt patches to new upstream version
---
debian/patches/10-build.xml.patch | 4 +-
debian/patches/11-snappy-java-compatibility.patch | 24 --
debian/patches/13-skip_network_tests | 366 +++++++++++-----------
debian/patches/20-fix-version.patch | 17 +-
debian/patches/50-fix-build.patch | 11 -
debian/patches/series | 2 -
6 files changed, 193 insertions(+), 231 deletions(-)
diff --git a/debian/patches/10-build.xml.patch b/debian/patches/10-build.xml.patch
index 9398f0f..6ed79eb 100644
--- a/debian/patches/10-build.xml.patch
+++ b/debian/patches/10-build.xml.patch
@@ -6,13 +6,13 @@ Last-Update: Wed, 29 Jun 2016 10:45:03 +0200
--- a/build.gradle
+++ b/build.gradle
-@@ -9,9 +9,6 @@ plugins {
+@@ -10,9 +10,6 @@ plugins {
id 'maven'
id 'signing'
id 'jacoco'
- id 'com.palantir.git-version' version '0.5.1'
- id 'com.github.johnrengelman.shadow' version '1.2.3'
-- id "com.github.kt3k.coveralls" version "2.6.3"
+- id 'com.github.maiflai.scalatest' version '0.15'
}
repositories {
diff --git a/debian/patches/11-snappy-java-compatibility.patch b/debian/patches/11-snappy-java-compatibility.patch
deleted file mode 100644
index a74f720..0000000
--- a/debian/patches/11-snappy-java-compatibility.patch
+++ /dev/null
@@ -1,24 +0,0 @@
-Description: Fix the compatibility with the latest version of snappy-java.
- The fix is Debian specific and assumes the native library is always available
- (which is true in Debian).
-Author: Emmanuel Bourg <ebourg at apache.org>
-Forwarded: not-needed
---- 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;
-
- import htsjdk.samtools.SAMException;
--import org.xerial.snappy.LoadSnappy;
- import org.xerial.snappy.SnappyInputStream;
-
- import java.io.InputStream;
-@@ -83,7 +82,7 @@ public class SnappyLoader {
- // Don't try to call any Snappy code until classes have been found via reflection above.
- boolean tmpSnappyAvailable;
- try {
-- if (!LoadSnappy.load()) {
-+ if (false) {
- if (verbose) System.err.println("Snappy dll failed to load.");
- tmpSnappyAvailable = false;
- }
diff --git a/debian/patches/13-skip_network_tests b/debian/patches/13-skip_network_tests
index c326879..27a487e 100644
--- a/debian/patches/13-skip_network_tests
+++ b/debian/patches/13-skip_network_tests
@@ -3,148 +3,9 @@ Subject: disable network tests
Description: remove network related tests
fixing bug 808593
Last-Updated: 2015-01-06
---- 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"));
- }
-
-- @Test
-- public void testFTPDoesExist() throws IOException{
-- tstExists(AVAILABLE_FTP_URL, true);
-- }
--
-- @Test
-- public void testFTPNotExist() throws IOException{
-- tstExists(UNAVAILABLE_FTP_URL, false);
-- }
--
-- @Test
-- public void testHTTPDoesExist() throws IOException{
-- tstExists(AVAILABLE_HTTP_URL, true);
-- }
--
-- @Test
-- public void testHTTPNotExist() throws IOException{
-- tstExists(UNAVAILABLE_HTTP_URL, false);
-- }
--
- private void tstExists(String path, boolean expectExists) throws IOException{
- boolean exists = ParsingUtils.resourceExists(path);
- Assert.assertEquals(exists, expectExists);
- }
-
-- @Test
-- public void testFTPOpenInputStream() throws IOException{
-- tstStream(AVAILABLE_FTP_URL);
-- }
--
-- @Test
-- public void testHTTPOpenInputStream() throws IOException{
-- tstStream(AVAILABLE_HTTP_URL);
-- }
-
-- private void tstStream(String path) throws IOException{
-- InputStream is = ParsingUtils.openInputStream(path);
-- Assert.assertNotNull(is, "InputStream is null for " + path);
-- int b = is.read();
-- Assert.assertNotSame(b, -1);
-- }
-
-
- }
---- a/src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java
-+++ b/src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java
-@@ -27,86 +27,4 @@ public class AbstractFeatureReaderTest {
- final static String HTTP_INDEXED_VCF_PATH = TestUtil.BASE_URL_FOR_HTTP_TESTS + "ex2.vcf";
- final static String LOCAL_MIRROR_HTTP_INDEXED_VCF_PATH = VariantBaseTest.variantTestDataRoot + "ex2.vcf";
-
-- /**
-- * Asserts readability and correctness of VCF over HTTP. The VCF is indexed and requires and index.
-- */
-- @Test
-- public void testVcfOverHTTP() throws IOException {
-- final VCFCodec codec = new VCFCodec();
-- final AbstractFeatureReader<VariantContext, LineIterator> featureReaderHttp =
-- AbstractFeatureReader.getFeatureReader(HTTP_INDEXED_VCF_PATH, codec, true); // Require an index to
-- final AbstractFeatureReader<VariantContext, LineIterator> featureReaderLocal =
-- AbstractFeatureReader.getFeatureReader(LOCAL_MIRROR_HTTP_INDEXED_VCF_PATH, codec, false);
-- final CloseableTribbleIterator<VariantContext> localIterator = featureReaderLocal.iterator();
-- for (final Feature feat : featureReaderHttp.iterator()) {
-- assertEquals(feat.toString(), localIterator.next().toString());
-- }
-- assertFalse(localIterator.hasNext());
-- }
--
-- @Test
-- public void testLoadBEDFTP() throws Exception {
-- final String path = "ftp://ftp.broadinstitute.org/distribution/igv/TEST/cpgIslands with spaces.hg18.bed";
-- final BEDCodec codec = new BEDCodec();
-- final AbstractFeatureReader<BEDFeature, LineIterator> bfs = AbstractFeatureReader.getFeatureReader(path, codec, false);
-- for (final Feature feat : bfs.iterator()) {
-- 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/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
+++ b/src/test/java/htsjdk/samtools/seekablestream/SeekableBufferedStreamTest.java
-@@ -40,58 +40,7 @@ public class SeekableBufferedStreamTest
+@@ -41,58 +41,7 @@ public class SeekableBufferedStreamTest
private final String BAM_URL_STRING = "http://broadinstitute.github.io/picard/testdata/index_test.bam";
private static File TestFile = new File("src/test/resources/htsjdk/samtools/seekablestream/megabyteZeros.dat");
@@ -674,9 +535,9 @@ Last-Updated: 2015-01-06
}
--- a/src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java
+++ b/src/test/java/htsjdk/tribble/util/ftp/FTPUtilsTest.java
-@@ -14,18 +14,4 @@ import static org.testng.Assert.assertTr
+@@ -15,18 +15,4 @@ import static org.testng.Assert.assertTr
*/
- public class FTPUtilsTest {
+ public class FTPUtilsTest extends HtsjdkTest {
- @Test
- public void testResourceAvailable() throws Exception {
@@ -695,7 +556,7 @@ Last-Updated: 2015-01-06
}
--- a/src/test/java/htsjdk/tribble/util/ftp/FTPClientTest.java
+++ b/src/test/java/htsjdk/tribble/util/ftp/FTPClientTest.java
-@@ -23,225 +23,4 @@ public class FTPClientTest {
+@@ -24,225 +24,4 @@ public class FTPClientTest extends Htsjd
static byte[] expectedBytes = "abcdefghijklmnopqrstuvwxyz\n".getBytes();
FTPClient client;
@@ -923,8 +784,8 @@ Last-Updated: 2015-01-06
}
--- a/src/test/java/htsjdk/samtools/seekablestream/SeekableFTPStreamTest.java
+++ b/src/test/java/htsjdk/samtools/seekablestream/SeekableFTPStreamTest.java
-@@ -38,68 +38,6 @@ import java.net.URL;
- public class SeekableFTPStreamTest {
+@@ -39,68 +39,6 @@ import java.net.URL;
+ public class SeekableFTPStreamTest extends HtsjdkTest {
- static String urlString = "ftp://ftp.broadinstitute.org/pub/igv/TEST/test.txt";
@@ -994,9 +855,9 @@ Last-Updated: 2015-01-06
--- a/src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java
+++ b/src/test/java/htsjdk/samtools/cram/ref/EnaRefServiceTest.java
-@@ -7,9 +7,4 @@ import java.io.IOException;
+@@ -8,9 +8,4 @@ import java.io.IOException;
- public class EnaRefServiceTest {
+ public class EnaRefServiceTest extends HtsjdkTest {
- @Test
- public void test() throws IOException, EnaRefService.GaveUpException {
@@ -1004,40 +865,10 @@ Last-Updated: 2015-01-06
- Assert.assertNotNull(new EnaRefService().getSequence("0000088cbcebe818eb431d58c908c698"));
- }
}
---- a/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java
-+++ b/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java
-@@ -136,27 +136,4 @@ public class TabixReaderTest {
-
- }
-
-- /**
-- * Test reading a tabix file over http
-- *
-- * @throws java.io.IOException
-- */
-- @Test
-- public void testRemoteQuery() throws IOException {
-- String tabixFile = TestUtil.BASE_URL_FOR_HTTP_TESTS +"igvdata/tabix/trioDup.vcf.gz";
--
-- TabixReader tabixReader = new TabixReader(tabixFile);
--
-- TabixIteratorLineReader lineReader = new TabixIteratorLineReader(
-- tabixReader.query(tabixReader.chr2tid("4"), 320, 330));
--
-- int nRecords = 0;
-- String nextLine;
-- while ((nextLine = lineReader.readLine()) != null) {
-- assertTrue(nextLine.startsWith("4"));
-- nRecords++;
-- }
-- assertTrue(nRecords > 0);
--
-- }
- }
--- a/src/test/java/htsjdk/samtools/BAMRemoteFileTest.java
+++ b/src/test/java/htsjdk/samtools/BAMRemoteFileTest.java
-@@ -43,285 +43,7 @@ import static org.testng.Assert.*;
- public class BAMRemoteFileTest {
+@@ -44,285 +44,7 @@ import static org.testng.Assert.*;
+ public class BAMRemoteFileTest extends HtsjdkTest {
private final File BAM_INDEX_FILE = new File("src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam.bai");
private final File BAM_FILE = new File("src/test/resources/htsjdk/samtools/BAMFileIndexTest/index_test.bam");
- private final String BAM_URL_STRING = TestUtil.BASE_URL_FOR_HTTP_TESTS + "index_test.bam";
@@ -1322,3 +1153,180 @@ Last-Updated: 2015-01-06
- }
- }
}
+--- a/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java
++++ b/src/test/java/htsjdk/tribble/readers/TabixReaderTest.java
+@@ -135,30 +135,6 @@ public class TabixReaderTest extends Hts
+ }
+
+ /**
+- * Test reading a tabix file over http
+- *
+- * @throws java.io.IOException
+- */
+- @Test
+- public void testRemoteQuery() throws IOException {
+- String tabixFile = TestUtil.BASE_URL_FOR_HTTP_TESTS +"igvdata/tabix/trioDup.vcf.gz";
+-
+- TabixReader tabixReader = new TabixReader(tabixFile);
+-
+- TabixIteratorLineReader lineReader = new TabixIteratorLineReader(
+- tabixReader.query(tabixReader.chr2tid("4"), 320, 330));
+-
+- int nRecords = 0;
+- String nextLine;
+- while ((nextLine = lineReader.readLine()) != null) {
+- Assert.assertTrue(nextLine.startsWith("4"));
+- nRecords++;
+- }
+- Assert.assertTrue(nRecords > 0);
+-
+- }
+-
+- /**
+ * Test TabixReader.readLine
+ *
+ * @throws java.io.IOException
+--- a/src/test/java/htsjdk/tribble/util/ParsingUtilsTest.java
++++ b/src/test/java/htsjdk/tribble/util/ParsingUtilsTest.java
+@@ -153,26 +153,6 @@ public class ParsingUtilsTest extends Ht
+ tstExists(file.toUri().toString(), false);
+ }
+
+- @Test
+- public void testFTPDoesExist() throws IOException{
+- tstExists(AVAILABLE_FTP_URL, true);
+- }
+-
+- @Test
+- public void testFTPNotExist() throws IOException{
+- tstExists(UNAVAILABLE_FTP_URL, false);
+- }
+-
+- @Test
+- public void testHTTPDoesExist() throws IOException{
+- tstExists(AVAILABLE_HTTP_URL, true);
+- }
+-
+- @Test
+- public void testHTTPNotExist() throws IOException{
+- tstExists(UNAVAILABLE_HTTP_URL, false);
+- }
+-
+ private void tstExists(String path, boolean expectExists) throws IOException{
+ boolean exists = ParsingUtils.resourceExists(path);
+ Assert.assertEquals(exists, expectExists);
+@@ -198,22 +178,5 @@ public class ParsingUtilsTest extends Ht
+ tstStream(file.toUri().toString());
+ }
+
+- @Test
+- public void testFTPOpenInputStream() throws IOException{
+- tstStream(AVAILABLE_FTP_URL);
+- }
+-
+- @Test
+- public void testHTTPOpenInputStream() throws IOException{
+- tstStream(AVAILABLE_HTTP_URL);
+- }
+-
+- private void tstStream(String path) throws IOException{
+- InputStream is = ParsingUtils.openInputStream(path);
+- Assert.assertNotNull(is, "InputStream is null for " + path);
+- int b = is.read();
+- Assert.assertNotSame(b, -1);
+- }
+-
+
+ }
+--- a/src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java
++++ b/src/test/java/htsjdk/tribble/AbstractFeatureReaderTest.java
+@@ -50,89 +50,6 @@ public class AbstractFeatureReaderTest e
+ //wrapper which skips the first byte of a file and leaves the rest unchanged
+ private static final Function<SeekableByteChannel, SeekableByteChannel> WRAPPER = SkippingByteChannel::new;
+
+- /**
+- * Asserts readability and correctness of VCF over HTTP. The VCF is indexed and requires and index.
+- */
+- @Test
+- public void testVcfOverHTTP() throws IOException {
+- final VCFCodec codec = new VCFCodec();
+- final AbstractFeatureReader<VariantContext, LineIterator> featureReaderHttp =
+- AbstractFeatureReader.getFeatureReader(HTTP_INDEXED_VCF_PATH, codec, true); // Require an index to
+- final AbstractFeatureReader<VariantContext, LineIterator> featureReaderLocal =
+- AbstractFeatureReader.getFeatureReader(LOCAL_MIRROR_HTTP_INDEXED_VCF_PATH, codec, false);
+- final CloseableTribbleIterator<VariantContext> localIterator = featureReaderLocal.iterator();
+- for (final Feature feat : featureReaderHttp.iterator()) {
+- assertEquals(feat.toString(), localIterator.next().toString());
+- }
+- assertFalse(localIterator.hasNext());
+- }
+-
+- @Test
+- public void testLoadBEDFTP() throws Exception {
+- final String path = "ftp://ftp.broadinstitute.org/distribution/igv/TEST/cpgIslands with spaces.hg18.bed";
+- final BEDCodec codec = new BEDCodec();
+- final AbstractFeatureReader<BEDFeature, LineIterator> bfs = AbstractFeatureReader.getFeatureReader(path, codec, false);
+- for (final Feature feat : bfs.iterator()) {
+- 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(dataProvider = "blockCompressedExtensionExtensionStrings")
+- public void testBlockCompressionExtensionString(final String testString, final boolean expected) {
+- Assert.assertEquals(AbstractFeatureReader.hasBlockCompressedExtension(testString), expected);
+- }
+-
+- @Test(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(dataProvider = "blockCompressedExtensionExtensionURIStrings")
+- public void testBlockCompressionExtension(final String testURIString, final boolean expected) throws URISyntaxException {
+- URI testURI = URI.create(testURIString);
+- Assert.assertEquals(AbstractFeatureReader.hasBlockCompressedExtension(testURI), expected);
+- }
+-
+-
+ @DataProvider(name = "vcfFileAndWrapperCombinations")
+ private static Object[][] vcfFileAndWrapperCombinations(){
+ return new Object[][] {
diff --git a/debian/patches/20-fix-version.patch b/debian/patches/20-fix-version.patch
index fe9b4e1..6209617 100644
--- a/debian/patches/20-fix-version.patch
+++ b/debian/patches/20-fix-version.patch
@@ -5,8 +5,8 @@ Forwarded: not-needed
Last-Updated: 2016-07-05
--- a/build.gradle
+++ b/build.gradle
-@@ -8,29 +8,12 @@
- id "java"
+@@ -9,24 +9,12 @@ plugins {
+ id 'scala'
id 'maven'
id 'signing'
- id 'jacoco'
@@ -17,25 +17,20 @@ Last-Updated: 2016-07-05
}
-jacocoTestReport {
-- dependsOn test
- group = "Reporting"
- description = "Generate Jacoco coverage reports after running tests."
- additionalSourceDirs = files(sourceSets.main.allJava.srcDirs)
-
- reports {
-- xml.enabled = true // coveralls plugin depends on xml format report
+- xml.enabled = true // codecov depends on xml format report
- html.enabled = true
- }
-}
-
--jacoco {
-- toolVersion = "0.7.5.201505241946"
--}
--
dependencies {
compile "org.apache.commons:commons-jexl:2.1.1"
compile "commons-logging:commons-logging:1.1.1"
-@@ -45,9 +28,17 @@
+@@ -45,9 +33,17 @@ dependencies {
sourceCompatibility = 1.8
targetCompatibility = 1.8
@@ -56,10 +51,6 @@ Last-Updated: 2016-07-05
logger.info("build for version:" + version)
group = 'com.github.samtools'
--- /dev/null
-+++ b/settings.gradle
-@@ -0,0 +1 @@
-+rootProject.name = rootName
---- /dev/null
+++ b/gradle.properties
@@ -0,0 +1 @@
+rootName=htsjdk
diff --git a/debian/patches/50-fix-build.patch b/debian/patches/50-fix-build.patch
deleted file mode 100644
index b7b6047..0000000
--- a/debian/patches/50-fix-build.patch
+++ /dev/null
@@ -1,11 +0,0 @@
-junit JAR is required for tests
---- a/build.gradle
-+++ b/build.gradle
-@@ -23,6 +23,7 @@
- compile "gov.nih.nlm.ncbi:ngs-java:1.2.4"
-
- testCompile "org.testng:testng:6.9.9"
-+ testCompile "junit:junit:4.x"
- }
-
- sourceCompatibility = 1.8
diff --git a/debian/patches/series b/debian/patches/series
index 52d46d3..aaaa071 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,5 +1,3 @@
10-build.xml.patch
-11-snappy-java-compatibility.patch
13-skip_network_tests
20-fix-version.patch
-50-fix-build.patch
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/htsjdk.git
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