[med-svn] [Git][med-team/igv][master] 3 commits: Solving ambiguity to build against htsjdk/4.0.2+dfsg

[Pierre Gruet (@pgt)]

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 <pgt at 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 <pgt at 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
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