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 <[email protected]> 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 <[email protected]> +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 You're receiving this email because of your account on salsa.debian.org.
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