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Error parsing line at byte position when uploading bed file #719

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olechnwin opened this issue Oct 25, 2019 · 1 comment
Closed

Error parsing line at byte position when uploading bed file #719

olechnwin opened this issue Oct 25, 2019 · 1 comment

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@olechnwin
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Hi,
I tried to open a bed file and it's giving me this error:

Error loading D:\macs2_rslt.bed: Error parsing line at byte position: LineIteratorImpl(SynchronousLineReader), for input source: D:\macs2_rslt.bed

This is the error in igv.log:

ERROR [2019-08-06T12:36:14,155] [DataPanel.java:253]  Error: 
java.util.concurrent.CompletionException: java.lang.NullPointerException
	at java.util.concurrent.CompletableFuture.encodeThrowable(Unknown Source) ~[?:?]
	at java.util.concurrent.CompletableFuture.completeThrowable(Unknown Source) ~[?:?]
	at java.util.concurrent.CompletableFuture$AsyncRun.run(Unknown Source) ~[?:?]
	at java.util.concurrent.ThreadPoolExecutor.runWorker(Unknown Source) ~[?:?]
	at java.util.concurrent.ThreadPoolExecutor$Worker.run(Unknown Source) ~[?:?]
	at java.lang.Thread.run(Unknown Source) ~[?:?]
Caused by: java.lang.NullPointerException
	at org.broad.igv.track.DataSourceTrack.getSummaryScores(DataSourceTrack.java:106) ~[igv.jar:?]
	at org.broad.igv.track.DataTrack.load(DataTrack.java:144) ~[igv.jar:?]
	at org.broad.igv.ui.panel.DataPanel.lambda$load$3(DataPanel.java:225) ~[igv.jar:?]
	... 4 more

I'm attaching the bed.file that's giving me this error.
Can you please help me figure out what was wrong? Thank you in advance.
macs2_rslt.zip
@olechnwin
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olechnwin commented Oct 28, 2019 •
edited
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I figured out what was wrong. In one of the bed line, the address was written in scientific form. That's why IGV is throwing out an error.

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@olechnwin