Bug#1058683: FTBFS against htsjdk/4.0.2+dfsg-1 now in unstable

[Pierre Gruet]

Source: igv
Version: 2.16.2+dfsg-1
Severity: serious
Tags: patch

Hello,

igv fails to build against new htsjdk/4.0.2+dfsg-1:

/<<PKGBUILDDIR>>/src/main/java/org/broad/igv/track/TribbleFeatureSource.java:352:
 error: reference to NamedFeature is ambiguous
                    if (f instanceof NamedFeature) 
FeatureDB.addFeature((NamedFeature) f, genome);
                                     ^
  both interface org.broad.igv.feature.NamedFeature in org.broad.igv.feature 
and interface htsjdk.tribble.NamedFeature in htsjdk.tribble match
/<<PKGBUILDDIR>>/src/main/java/org/broad/igv/track/TribbleFeatureSource.java:352:
 error: reference to NamedFeature is ambiguous
                    if (f instanceof NamedFeature) 
FeatureDB.addFeature((NamedFeature) f, genome);
                                                                         ^
  both interface org.broad.igv.feature.NamedFeature in org.broad.igv.feature 
and interface htsjdk.tribble.NamedFeature in htsjdk.tribble match

There is some ambiguity to be removed, which is solved by the enclosed patch.

Best,

-- 
Pierre

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: no
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;