[med-svn] [artemis] 01/01: Cleanup patches and add DEP3 headers
Andreas Tille
tille at debian.org
Thu Dec 8 08:22:10 UTC 2016
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to branch master
in repository artemis.
commit 5636cf8f3d0dbec23e280aefaecc7649a94f5e63
Author: Andreas Tille <tille at debian.org>
Date: Thu Dec 8 09:21:45 2016 +0100
Cleanup patches and add DEP3 headers
---
debian/changelog | 4 ++
debian/patches/CRAMReferenceSequenceFile.patch | 21 ----------
debian/patches/htsjdk-api-change.patch | 3 ++
debian/patches/java-8-sort.patch | 57 --------------------------
debian/patches/samreader.patch | 6 +++
debian/patches/use-lang3.patch | 4 ++
6 files changed, 17 insertions(+), 78 deletions(-)
diff --git a/debian/changelog b/debian/changelog
index 7d37907..f259818 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,10 +1,14 @@
artemis (16.0.17+dfsg-1) UNRELEASED; urgency=medium
+ [ Sascha Steinbiss ]
* Team upload.
* New upstream release.
* Refresh patches.
* Avoid use of deprecated SAM access method to fix FTBFS.
+ [ Andreas Tille ]
+ * Cleanup patches and add DEP3 headers
+
-- Sascha Steinbiss <satta at debian.org> Wed, 07 Dec 2016 22:19:05 +0000
artemis (16.0.0+dfsg-5) unstable; urgency=medium
diff --git a/debian/patches/CRAMReferenceSequenceFile.patch b/debian/patches/CRAMReferenceSequenceFile.patch
deleted file mode 100644
index 1ccb12e..0000000
--- a/debian/patches/CRAMReferenceSequenceFile.patch
+++ /dev/null
@@ -1,21 +0,0 @@
-Description: Override abstract method
- Compilation otherwise fails (at least using dependencies from Debian packages)
- because an abstract class is not overridden. This patch provides a simple
- override of the offending method
-Author: Afif Elghraoui <afif at ghraoui.name>
-Forwarded: https://github.com/sanger-pathogens/Artemis/pull/218
-Last-Update: 2015-10-22
---- artemis.orig/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java
-+++ artemis/uk/ac/sanger/artemis/components/alignment/CRAMReferenceSequenceFile.java
-@@ -107,5 +107,8 @@
- public void reset()
- {
- }
--
-- }
-\ No newline at end of file
-+
-+ public void close()
-+ {
-+ }
-+ }
diff --git a/debian/patches/htsjdk-api-change.patch b/debian/patches/htsjdk-api-change.patch
index f05d5ee..4de961d 100644
--- a/debian/patches/htsjdk-api-change.patch
+++ b/debian/patches/htsjdk-api-change.patch
@@ -1,5 +1,8 @@
Description: adjust log configuration to new API
Author: Sascha Steinbiss <sascha at steinbiss.name>
+Bug-Debian: https://bugs.debian.org/808851
+Last-Update: 2016-03-25 11:24:07 +0000
+
--- a/uk/ac/sanger/artemis/components/alignment/BamView.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamView.java
@@ -116,7 +116,7 @@
diff --git a/debian/patches/java-8-sort.patch b/debian/patches/java-8-sort.patch
deleted file mode 100644
index dc384d5..0000000
--- a/debian/patches/java-8-sort.patch
+++ /dev/null
@@ -1,57 +0,0 @@
-Description: fix name clash with Java 8 List.sort()
-Author: Sascha Steinbiss <sascha at steinbiss.name>
---- a/uk/ac/sanger/artemis/AlignMatchVector.java
-+++ b/uk/ac/sanger/artemis/AlignMatchVector.java
-@@ -107,7 +107,7 @@
- * @param cmp The returned vector will be sorted with this Comparator.
- **/
- public void sort (final Comparator cmp) {
-- vector = vector.sort (cmp);
-+ vector = vector.mysort (cmp);
- }
-
- /**
---- a/uk/ac/sanger/artemis/FeatureVector.java
-+++ b/uk/ac/sanger/artemis/FeatureVector.java
-@@ -154,7 +154,7 @@
- public FeatureVector sort (final Comparator cmp) {
- final FeatureVector return_vector = (FeatureVector) clone ();
-
-- return_vector.vector = return_vector.vector.sort (cmp);
-+ return_vector.vector = return_vector.vector.mysort (cmp);
-
- return return_vector;
- }
---- a/uk/ac/sanger/artemis/io/KeyVector.java
-+++ b/uk/ac/sanger/artemis/io/KeyVector.java
-@@ -65,7 +65,7 @@
- * Sorts the elements of the vector using a simple O(n^2) selection
- * sort.
- */
-- public void sort()
-+ public void mysort()
- {
- int smallest;
-
---- a/uk/ac/sanger/artemis/io/SimpleEntryInformation.java
-+++ b/uk/ac/sanger/artemis/io/SimpleEntryInformation.java
-@@ -175,7 +175,7 @@
- return null;
- }
-
-- return_vector.sort ();
-+ return_vector.mysort ();
- return return_vector;
- }
-
---- a/uk/ac/sanger/artemis/util/FastVector.java
-+++ b/uk/ac/sanger/artemis/util/FastVector.java
-@@ -91,7 +91,7 @@
- * Return a sorted copy of this vector.
- * @param cmp The returned vector will be sorted with this Comparator.
- **/
-- public FastVector sort(final Comparator cmp)
-+ public FastVector mysort(final Comparator cmp)
- {
- final FastVector return_vector = (FastVector)clone();
- Collections.sort(return_vector, cmp);
diff --git a/debian/patches/samreader.patch b/debian/patches/samreader.patch
index d81535c..6353b9b 100644
--- a/debian/patches/samreader.patch
+++ b/debian/patches/samreader.patch
@@ -1,3 +1,9 @@
+Description: Implement new htsjdk API
+ See https://github.com/samtools/htsjdk/issues/767#issuecomment-264864910
+Author: Sascha Steinbiss <sascha at steinbiss.name>
+Bug-Debian: https://bugs.debian.org/846671
+Last-Update: 2016-12-07 23:37:52 +0000
+
--- a/uk/ac/sanger/artemis/components/alignment/BamUtils.java
+++ b/uk/ac/sanger/artemis/components/alignment/BamUtils.java
@@ -31,7 +31,7 @@
diff --git a/debian/patches/use-lang3.patch b/debian/patches/use-lang3.patch
index 4441b30..04e7a16 100644
--- a/debian/patches/use-lang3.patch
+++ b/debian/patches/use-lang3.patch
@@ -1,3 +1,7 @@
+Description: use lang3
+Author: Sascha Steinbiss
+Last-Update: 2016-12-07 23:37:09 +0000
+
--- a/uk/ac/sanger/artemis/io/GFF3Encoder.java
+++ b/uk/ac/sanger/artemis/io/GFF3Encoder.java
@@ -22,7 +22,7 @@
--
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