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igvteam / igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations
https://igv.org
MIT License
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unexpecgted error repainintg view #1024

Closed wjyzidane closed 3 years ago

wjyzidane commented 3 years ago

Hello,

I am using the IGV(2.11.0) to view a region has about 20-30 reads in bam. When I zoom in, it gives me "unexpected error repainting view" error and no reads at all.

jrobinso commented 3 years ago

I'll need more information than that to help you. We could start with the "igv.log" file, located in the igv folder in your home directory. If you can reproduce this with public data and share exact steps to reproduce that would be helpful also.

wjyzidane commented 3 years ago

Hello,

Here is the message from igv.log : ERROR [2021-09-09T18:06:08,620] [DataPanel.java:174] Error painting DataPanel java.lang.NullPointerException: null

and attached are the reads for that region in bam (it gives me the same error): blood_chr2_87196925_87619276.bam.zip

jrobinso commented 3 years ago

I can't reproduce it with that data (see screenshot). Do you have any custom igv settings? If so what are they?

If you zip and attach the whole log so I can see the stack trace I will look into this further, also if you have custom settings or can't recall if you do please zip and attach the "pref.properties" file in the igv folder.

Screen Shot 2021-09-09 at 4 08 34 PM
wjyzidane commented 3 years ago

Please find them attached. Thanks! igv.log.zip prefs.properties.zip

jrobinso commented 3 years ago

I just pushed a change that should fix this, based on your log file. I can't be sure since I still can't reproduce it, and you have not provided me with steps to reproduce. The fix will be in the next release, probably early next week.

BTW your log indicates you are viewing this data in bisulfite mode, but the data does not appear to be from bisulfite sequencing. This should not cause an error, but is unusual.