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JetBrains-Research / jbr

JBR Genome Browser
https://doi.org/10.1093/bioinformatics/btab376
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Cannot invoke "htsjdk.samtools.SAMRecord.getAlignmentStart()" because "mate" is null #224

Closed iromeo closed 1 year ago

iromeo commented 1 year ago 
Caused by: ERROR NullPointerException Cannot invoke "htsjdk.samtools.SAMRecord.getAlignmentStart()" because "mate" is null
org.jetbrains.bio.browser.bam.readers.SamRecordsDiscReader.getReadsPaired(SamRecordsDiscReader.kt:104)
org.jetbrains.bio.browser.bam.BamTrackView$getReadsPaired$1.invoke(BamTrackView.kt:200)
org.jetbrains.bio.browser.bam.BamTrackView$getReadsPaired$1.invoke(BamTrackView.kt:197)
org.jetbrains.bio.browser.bam.BamTrackView.ensureSrcAccessible(BamTrackView.kt:161)
org.jetbrains.bio.browser.bam.BamTrackView.getReadsPaired(BamTrackView.kt:197)
org.jetbrains.bio.browser.bam.BamTrackView.initConfig(BamTrackView.kt:268)
org.jetbrains.bio.browser.tracks.TrackViewRenderer.initConfigAndPrepareScales(TrackViewRenderer.kt:109)
org.jetbrains.bio.browser.desktop.TrackViewRenderComponent$restart$1$1.invoke(TrackViewRenderComponent.kt:97)
org.jetbrains.bio.browser.desktop.TrackViewRenderComponent$restart$1$1.invoke(TrackViewRenderComponent.kt:95)
org.jetbrains.bio.util.LoggerExtensionsKt.time(LoggerExtensions.kt:20)
org.jetbrains.bio.browser.desktop.TrackViewRenderComponent.restart$lambda-2(TrackViewRenderComponent.kt:95)
org.jetbrains.bio.util.CancellableTask.execute$lambda-1(Cancellable.kt:108)
java.base/java.util.concurrent.FutureTask.run$$$capture(FutureTask.java:264)
java.base/java.util.concurrent.FutureTask.run(FutureTask.java)
java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
java.base/java.lang.Thread.run(Thread.java:833)

Location: hg38 chr11:11798158-11800146 File: FA06_hg38_pe.bam.chr11.by_name.sorted.bam Branch: 024ed1d85902d4122bf455c597f6d371cc75519d