[med-svn] [htsjdk] 05/06: Adapt patches

[Andreas Tille]

This is an automated email from the git hooks/post-receive script.

tille pushed a commit to branch master
in repository htsjdk.

commit ecc9037903eac01f8322776558101b9a75ff4856
Author: Andreas Tille <tille at debian.org>
Date:   Sat Dec 19 21:50:03 2015 +0100

    Adapt patches
---
 debian/patches/01-for-upstream-fix-version-in-manifest | 16 ----------------
 debian/patches/10-build.xml                            |  4 ++--
 debian/patches/11-snappy-java-compatibility.patch      |  2 +-
 debian/patches/12-use_libjbzip2-java                   |  4 ++--
 debian/patches/series                                  |  1 -
 5 files changed, 5 insertions(+), 22 deletions(-)

diff --git a/debian/patches/01-for-upstream-fix-version-in-manifest b/debian/patches/01-for-upstream-fix-version-in-manifest
deleted file mode 100644
index 7b83d3c..0000000
--- a/debian/patches/01-for-upstream-fix-version-in-manifest
+++ /dev/null
@@ -1,16 +0,0 @@
-Description: fix the 'Implementation-Version' in MANIFEST
- This patch fix the typo in the used property name for the
- Implementation-Version value in MANIFEST
-Origin: vendor
-Forwarded: no
---- a/build.xml
-+++ b/build.xml
-@@ -177,7 +177,7 @@
-             <fileset dir="${classes}" includes="htsjdk/tribble/**/*.*"/>
-             <fileset dir="${classes}" includes="htsjdk/variant/**/*.*"/>
-             <manifest>
--                <attribute name="Implementation-Version" value="${hts-version}(${repository.revision})"/>
-+                <attribute name="Implementation-Version" value="${htsjdk-version}(${repository.revision})"/>
-                 <attribute name="Implementation-Vendor" value="Broad Institute"/>
-             </manifest>
-         </jar>
diff --git a/debian/patches/10-build.xml b/debian/patches/10-build.xml
index 5eca8e2..10e2b8e 100644
--- a/debian/patches/10-build.xml
+++ b/debian/patches/10-build.xml
@@ -13,7 +13,7 @@ Forwarded: no
  
 -    <property name="repository.revision" value=""/>
 +    <property name="repository.revision" value="dfsg"/>
-     <property name="htsjdk-version" value="1.138"/>
+     <property name="htsjdk-version" value="2.0.1"/>
      <property name="htsjdk-version-file" value="htsjdk.version.properties"/>
      <property name="testng.verbosity" value="2"/>
 @@ -72,6 +72,11 @@
@@ -36,7 +36,7 @@ Forwarded: no
              </classpath>
              <classfileset dir="${classes.test}">
                  <include name="**/Test*.class"/>
-@@ -203,8 +209,13 @@
+@@ -204,8 +210,13 @@
                  <fileset dir="${lib}">
                      <include name="**/*.jar" />
                  </fileset>
diff --git a/debian/patches/11-snappy-java-compatibility.patch b/debian/patches/11-snappy-java-compatibility.patch
index 6ecb83b..23fe89c 100644
--- a/debian/patches/11-snappy-java-compatibility.patch
+++ b/debian/patches/11-snappy-java-compatibility.patch
@@ -13,7 +13,7 @@ Forwarded: not-needed
  import org.xerial.snappy.SnappyInputStream;
  
  import java.io.InputStream;
-@@ -83,7 +82,7 @@
+@@ -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 {
diff --git a/debian/patches/12-use_libjbzip2-java b/debian/patches/12-use_libjbzip2-java
index d3552f1..9d602e2 100644
--- a/debian/patches/12-use_libjbzip2-java
+++ b/debian/patches/12-use_libjbzip2-java
@@ -7,7 +7,7 @@ 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 @@
+@@ -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;
@@ -16,7 +16,7 @@ Forwarded: not-needed
  
  import java.io.ByteArrayInputStream;
  import java.io.ByteArrayOutputStream;
-@@ -74,7 +74,7 @@
+@@ -74,7 +74,7 @@ public class ExternalCompression {
          // hello, apache!
          byteArrayInputStream.read();
          byteArrayInputStream.read();
diff --git a/debian/patches/series b/debian/patches/series
index d958e0b..3b37e27 100644
--- a/debian/patches/series
+++ b/debian/patches/series
@@ -1,4 +1,3 @@
-01-for-upstream-fix-version-in-manifest
 10-build.xml
 11-snappy-java-compatibility.patch
 12-use_libjbzip2-java

-- 
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