IGV 2.19.5 flickering while loading tracks

[Adam Clayton]

I'm trying to isolate what I think is a bug in the latest version(s) of the IGV desktop app (2.19.3-5) for windows that includes java. I'm using hg19 and loading reads/coverage, and a variety of bed and bedgraph files from AWS and I'm seeing IGV flicker as each of these tracks are loaded. I've attached a short video of the flickering and a screenshot of the image that keeps flickering on the screen. The igv.log file doesn't show any errors except for when I try to load a mitochondrial variant that specifies a specific chromosome build like "NC_012920:1,418-1,457"

Let me know if I can provide anything else to find the cause of the flickering.

Log output:

SEVERE [Jul 31,2025 11:44] [AlignmentDataManager] Error inferring alignment type
SEVERE [Jul 31,2025 11:44] [AlignmentDataManager] java.lang.IllegalArgumentException: Failure getting reference bases for sequence 1
at hts...@4.3.0-module/htsjdk.samtools.cram.build.CRAMReferenceRegion.fetchReferenceBasesByRegion(CRAMReferenceRegion.java:175)
at hts...@4.3.0-module/htsjdk.samtools.cram.build.CRAMReferenceRegion.fetchReferenceBasesByRegion(CRAMReferenceRegion.java:195)
at hts...@4.3.0-module/htsjdk.samtools.cram.structure.Slice.normalizeCRAMRecords(Slice.java:456)
at hts...@4.3.0-module/htsjdk.samtools.cram.structure.Container.getSAMRecords(Container.java:322)
at hts...@4.3.0-module/htsjdk.samtools.CRAMIterator.nextContainer(CRAMIterator.java:112)
at hts...@4.3.0-module/htsjdk.samtools.CRAMIterator.hasNext(CRAMIterator.java:204)
at hts...@4.3.0-module/htsjdk.samtools.SamReader$AssertingIterator.hasNext(SamReader.java:608)
at org.igv/org.broad.igv.sam.reader.WrappedIterator.hasNext(WrappedIterator.java:49)
at org.igv/org.broad.igv.sam.AlignmentUtils.firstAlignments(AlignmentUtils.java:243)
at org.igv/org.broad.igv.sam.AlignmentDataManager.inferType(AlignmentDataManager.java:385)
at org.igv/org.broad.igv.sam.AlignmentDataManager.<init>(AlignmentDataManager.java:91)
at org.igv/org.broad.igv.track.TrackLoader.loadAlignmentsTrack(TrackLoader.java:898)
at org.igv/org.broad.igv.track.TrackLoader.load(TrackLoader.java:198)
at org.igv/org.broad.igv.ui.IGV.load(IGV.java:1277)
at org.igv/org.broad.igv.ui.IGV.loadResources(IGV.java:1202)
at org.igv/org.broad.igv.ui.IGV$2.run(IGV.java:383)
at org.igv/org.broad.igv.util.LongRunningTask.submit(LongRunningTask.java:57)
at org.igv/org.broad.igv.ui.IGV.loadTracks(IGV.java:394)
at org.igv/org.broad.igv.batch.CommandExecutor.loadFiles(CommandExecutor.java:816)
at org.igv/org.broad.igv.batch.CommandListener.processGet(CommandListener.java:427)
at org.igv/org.broad.igv.batch.CommandListener.processClientSession(CommandListener.java:249)
at org.igv/org.broad.igv.batch.CommandListener.run(CommandListener.java:140)
at java.base/java.lang.Thread.run(Unknown Source)

[igv-help]

Its hard to gather any information from a 4 second video but that looks odd.   I have no idea what would cause that or how to reproduce it.   So you don't see this issue with IGV 2.19.2?