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JetBrains-Research / big

BigWIG, BigBED and TDF for the JVM
MIT License
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Tdf file reading: Buffer overflow: pos 601174837 > limit 601174836, max length: 601174836 #38

Open iromeo opened 6 years ago

iromeo commented 6 years ago

Download file https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE63874&format=file&file=GSE63874%5FNa%5FK2%5Fall%5Fminus%5Fcov%2Etdf and try to open "chr1:118808302-124161774"

big 0.8.0 unreleased

600873675 in 600873675..601001675
!!! 600873675 80 [600873675..601001675)
[Apr 25, 2018 03:04:35 ERROR RenderComponent] java.lang.IllegalStateException: Buffer overflow: pos 601174837 > limit 601174836, max length: 601174836
Caused by: ERROR Buffer overflow: pos 601174837 > limit 601174836, max length: 601174836
java.lang.IllegalStateException: Buffer overflow: pos 601174837 > limit 601174836, max length: 601174836
    at org.jetbrains.bio.RomBuffer.checkLimit(RomBuffer.kt:79)
    at org.jetbrains.bio.LightweightRomBuffer.readByte(LightweightRomBuffer.kt:58)
    at org.jetbrains.bio.SynchronizedStreamAccessRomBuffer.readByte(SynchronizedStreamAccessRomBuffer.kt:62)
    at org.jetbrains.bio.RomBuffer.readCString(RomBuffer.kt:64)
    at org.jetbrains.bio.tdf.TdfMasterIndex$Companion$readIndex$1.invoke(TdfFile.kt:284)
    at org.jetbrains.bio.tdf.TdfMasterIndex$Companion$readIndex$1.invoke(TdfFile.kt:281)
    at org.jetbrains.bio.tdf.TdfFileKt$getSequenceOf$$inlined$mapUnboxed$1.next(Support.kt:150)
    at kotlin.collections.MapsKt__MapsKt.putAll(Maps.kt:346)
    at kotlin.collections.MapsKt__MapsKt.toMap(Maps.kt:511)
    at kotlin.collections.MapsKt__MapsKt.toMap(Maps.kt:505)
    at org.jetbrains.bio.tdf.TdfMasterIndex$Companion.readIndex(TdfFile.kt:288)
    at org.jetbrains.bio.tdf.TdfMasterIndex$Companion.read(TdfFile.kt:292)
    at org.jetbrains.bio.tdf.TdfFile$Companion$read$2$index$1.invoke(TdfFile.kt:239)
    at org.jetbrains.bio.tdf.TdfFile$Companion$read$2$index$1.invoke(TdfFile.kt:203)
    at org.jetbrains.bio.RomBuffer.with$big(RomBuffer.kt:90)
    at org.jetbrains.bio.RomBuffer.with$big$default(RomBuffer.kt:89)
    at org.jetbrains.bio.tdf.TdfFile$Companion.read(TdfFile.kt:238)
    at org.jetbrains.bio.BigUtilKt.open(BigUtil.kt:30)
    at org.jetbrains.bio.browser.tracks.impl.TdfTrackView.preprocessImpl(TdfTrackView.kt:36)
    at org.jetbrains.bio.browser.tracks.TrackView.preprocess(TrackView.kt:147)
    at org.jetbrains.bio.browser.GenomeBrowser$preprocess$$inlined$mapIndexed$lambda$1.call(GenomeBrowser.kt:281)
    at org.jetbrains.bio.browser.GenomeBrowser$preprocess$$inlined$mapIndexed$lambda$1.call(GenomeBrowser.kt:34)
    at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
    at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:57)
    at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
    at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
    at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
    at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
    at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
    at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

227512595 in 227395404..227523404
!!! 227512595 80 [227395404..227523404)
[Apr 25, 2018 03:04:35 ERROR RenderComponent] java.lang.IllegalStateException: Unexpected header magic: Actual -2003829722 doesn't match expected LE=610839776 (BE=-525572060)
Caused by: ERROR Unexpected header magic: Actual -2003829722 doesn't match expected LE=610839776 (BE=-525572060)
java.lang.IllegalStateException: Unexpected header magic: Actual -2003829722 doesn't match expected LE=610839776 (BE=-525572060)
    at org.jetbrains.bio.RomBuffer.checkHeader(RomBuffer.kt:35)
    at org.jetbrains.bio.big.RTreeIndex$Header$Companion.read$big(RTreeIndex.kt:179)
    at org.jetbrains.bio.big.RTreeIndex$Companion.read$big(RTreeIndex.kt:203)
    at org.jetbrains.bio.big.BigFile.<init>(BigFile.kt:121)
    at org.jetbrains.bio.big.BigWigFile.<init>(BigWig.kt:18)
    at org.jetbrains.bio.big.BigWigFile.<init>(BigWig.kt:12)
    at org.jetbrains.bio.big.BigWigFile$Companion.read(BigWig.kt:181)
    at org.jetbrains.bio.BigUtilKt.open(BigUtil.kt:18)
    at org.jetbrains.bio.browser.tracks.impl.BigWigTrackView.preprocessImpl(BigWigTrackView.kt:91)
    at org.jetbrains.bio.browser.tracks.TrackView.preprocess(TrackView.kt:147)
    at org.jetbrains.bio.browser.GenomeBrowser$preprocess$$inlined$mapIndexed$lambda$1.call(GenomeBrowser.kt:281)
    at org.jetbrains.bio.browser.GenomeBrowser$preprocess$$inlined$mapIndexed$lambda$1.call(GenomeBrowser.kt:34)
    at com.google.common.util.concurrent.TrustedListenableFutureTask$TrustedFutureInterruptibleTask.runInterruptibly(TrustedListenableFutureTask.java:125)
    at com.google.common.util.concurrent.InterruptibleTask.run(InterruptibleTask.java:57)
    at com.google.common.util.concurrent.TrustedListenableFutureTask.run(TrustedListenableFutureTask.java:78)
    at java.util.concurrent.ForkJoinTask$RunnableExecuteAction.exec(ForkJoinTask.java:1402)
    at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
    at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
    at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
    at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)

600873675 in 600873675..601001675
!!! 600873675 80 [600873675..601001675)
227512595 in 227395404..227523404
!!! 227512595 80 [227395404..227523404)
[Apr 25, 2018 03:04:35 ERROR RenderComponent] offset 1294247056 out of range: 1294247056 not in [118808302, 124161774)
Caused by: ERROR offset 1294247056 out of range: 1294247056 not in [118808302, 124161774)
java.lang.IllegalArgumentException: offset 1294247056 out of range: 1294247056 not in [118808302, 124161774)
    at org.jetbrains.bio.browser.util.TrackUIUtil.genomeToScreen(TrackUIUtil.kt:426)
    at org.jetbrains.bio.browser.tracks.impl.TdfTrackView.paintTrackImpl(TdfTrackView.kt:53)
    at org.jetbrains.bio.browser.tracks.TrackView.paintTrack(TrackView.kt:194)
    at org.jetbrains.bio.browser.util.TrackViewRenderer.renderSingleLocationModel(TrackViewRenderer.kt:76)
    at org.jetbrains.bio.browser.util.TrackViewRenderer.paintToImage(TrackViewRenderer.kt:54)
    at org.jetbrains.bio.browser.util.TrackViewRenderer.paintToImage$default(TrackViewRenderer.kt:35)
    at org.jetbrains.bio.browser.desktop.RenderComponent$restart$1.call(RenderComponent.kt:72)
    at org.jetbrains.bio.browser.desktop.RenderComponent$restart$1.call(RenderComponent.kt:28)
    at org.jetbrains.bio.CancellableTask$execute$1.call(CancellableTask.kt:47)
    at java.util.concurrent.ForkJoinTask$AdaptedCallable.exec(ForkJoinTask.java:1424)
    at java.util.concurrent.ForkJoinTask.doExec(ForkJoinTask.java:289)
    at java.util.concurrent.ForkJoinPool$WorkQueue.runTask(ForkJoinPool.java:1056)
    at java.util.concurrent.ForkJoinPool.runWorker(ForkJoinPool.java:1692)
    at java.util.concurrent.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:157)