[med-svn] [Git][med-team/artemis][master] 5 commits: Adding a method definition to comply with htsjdk 3.0.2

[Pierre Gruet (@pgt)]

Pierre Gruet pushed to branch master at Debian Med / artemis


Commits:
44298d18 by Pierre Gruet at 2022-11-03T21:15:39+01:00
Adding a method definition to comply with htsjdk 3.0.2

- - - - -
5d9e5d38 by Pierre Gruet at 2022-11-03T21:15:55+01:00
Adding a versioned dependency on libhtsjdk-java

- - - - -
139053c7 by Pierre Gruet at 2022-11-03T21:17:07+01:00
Updating changelog

- - - - -
f4ad03e9 by Pierre Gruet at 2022-11-03T21:17:46+01:00
Raising Standards version to 4.6.1

- - - - -
961c734a by Pierre Gruet at 2022-11-04T11:10:32+01:00
Upload to unstable

- - - - -


4 changed files:

- debian/changelog
- debian/control
- + debian/patches/overriding_testReferenceBasesByRegion.patch
- debian/patches/series


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,13 @@
+artemis (18.2.0+dfsg-3) unstable; urgency=medium
+
+  * Raising Standards version to 4.6.1 (no change)
+  * Updating d/watch after changes in the Github layout
+  * Complying with htsjdk 3.0.2:
+    - Adding a method definition to extend an abstract class
+    - Adding a versioned dependency on libhtsjdk-java
+
+ -- Pierre Gruet <pgt at debian.org>  Fri, 04 Nov 2022 11:10:17 +0100
+
 artemis (18.2.0+dfsg-2) unstable; urgency=medium
 
   * Upload to unstable to accompany auto-biojava-live transition


=====================================
debian/control
=====================================
@@ -20,7 +20,7 @@ Build-Depends: debhelper-compat (= 13),
                liblog4j1.2-java,
                libpostgresql-jdbc-java,
                libpicard-java,
-               libhtsjdk-java,
+               libhtsjdk-java (>= 3.0.2+dfsg),
                libcommons-net-java,
                libcommons-lang3-java,
                libcommons-logging-java,
@@ -34,7 +34,7 @@ Build-Depends: debhelper-compat (= 13),
                libjs-jquery,
 # To convert gifs to png because gif is not a supported icon format
                imagemagick
-Standards-Version: 4.6.0
+Standards-Version: 4.6.1
 Vcs-Browser: https://salsa.debian.org/med-team/artemis
 Vcs-Git: https://salsa.debian.org/med-team/artemis.git
 Homepage: https://sanger-pathogens.github.io/Artemis/Artemis/


=====================================
debian/patches/overriding_testReferenceBasesByRegion.patch
=====================================
@@ -0,0 +1,23 @@
+Description: since htsjdk 3.0.2, we have to provide an override of this method.
+ Still, its behaviour is undefined and we raise an exception if it is called.
+Author: Pierre Gruet <pgt at debian.org>
+Forwarded: no
+Last-Update: 2022-11-03
+
+--- a/src/main/java/uk/ac/sanger/artemis/cramtools/ref/ReferenceSource.java
++++ b/src/main/java/uk/ac/sanger/artemis/cramtools/ref/ReferenceSource.java
+@@ -139,6 +139,14 @@
+ 		return bases;
+ 	}
+ 
++    @Override
++    public synchronized byte[] getReferenceBasesByRegion(
++            final SAMSequenceRecord sequenceRecord,
++            final int zeroBasedStart,
++            final int requestedRegionLength) {
++        throw new IllegalArgumentException("This method is not supported.");
++    }
++
+ 	private static byte[] readBytesFromFile(File file, int offset, int len) throws IOException {
+ 		long size = file.length();
+ 		if (size < offset || len < 0) {


=====================================
debian/patches/series
=====================================
@@ -5,3 +5,4 @@ no_install_of_provided_jars.patch
 running_build_tests.patch
 debianize_launcher_scripts.patch
 fix_surefire_argline.patch
+overriding_testReferenceBasesByRegion.patch



View it on GitLab: https://salsa.debian.org/med-team/artemis/-/compare/0d039b5c910dec81804834b767e44ba5a2f1d2d5...961c734af0b8238cfebf16a26c30dc44ee4844fd

-- 
View it on GitLab: https://salsa.debian.org/med-team/artemis/-/compare/0d039b5c910dec81804834b767e44ba5a2f1d2d5...961c734af0b8238cfebf16a26c30dc44ee4844fd
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