Pierre Gruet pushed to branch master at Debian Med / igv
Commits: e2cbbc08 by Pierre Gruet at 2023-12-14T14:03:40+01:00 Solving ambiguity to build against htsjdk/4.0.2+dfsg - - - - - 37f24af8 by Pierre Gruet at 2023-12-14T14:08:10+01:00 Updating changelog - - - - - 955a07cc by Pierre Gruet at 2023-12-14T14:09:11+01:00 Upload to unstable - - - - - 3 changed files: - debian/changelog - + debian/patches/htsjdk4.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,9 @@ +igv (2.16.2+dfsg-2) unstable; urgency=medium + + * Solving ambiguity to build against htsjdk/4.0.2+dfsg (Closes: #1058683) + + -- Pierre Gruet <p...@debian.org> Thu, 14 Dec 2023 14:09:05 +0100 + igv (2.16.2+dfsg-1) unstable; urgency=medium * New upstream version 2.16.2+dfsg ===================================== debian/patches/htsjdk4.patch ===================================== @@ -0,0 +1,17 @@ +Description: solving an ambiguity in the tests due to a new class in + htsjdk/4.0.2+dfsg +Author: Pierre Gruet <p...@debian.org> +Forwarded: https://github.com/igvteam/igv/issues/1461 +Last-Update: 2023-12-14 + +--- a/src/main/java/org/broad/igv/track/TribbleFeatureSource.java ++++ b/src/main/java/org/broad/igv/track/TribbleFeatureSource.java +@@ -349,7 +349,7 @@ + featureMap.put(igvChr, featureList); + } + featureList.add(f); +- if (f instanceof NamedFeature) FeatureDB.addFeature((NamedFeature) f, genome); ++ if (f instanceof org.broad.igv.feature.NamedFeature) FeatureDB.addFeature((org.broad.igv.feature.NamedFeature) f, genome); + + if (this.isVCF && f instanceof Variant) { + Variant v = (Variant) f; ===================================== debian/patches/series ===================================== @@ -5,3 +5,4 @@ old_gradle_name.patch jide_dependency.patch omit_aws_stuff.patch wrong_override.patch +htsjdk4.patch View it on GitLab: https://salsa.debian.org/med-team/igv/-/compare/244c4b242270dd75c32174a6718a8100962a5e9b...955a07ccd4629ec1cfebfae7e183c040e4406a7c -- View it on GitLab: https://salsa.debian.org/med-team/igv/-/compare/244c4b242270dd75c32174a6718a8100962a5e9b...955a07ccd4629ec1cfebfae7e183c040e4406a7c You're receiving this email because of your account on salsa.debian.org.
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