#1469 closed defect (fixed)

Update VarDict to version 1.8.3

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Reggie v4.45.1
Component: net.sf.basedb.reggie Keywords:
Cc:

Description

The Variant calling script crashed due to a bug in VarDict:

There was Exception while processing cigar on 25001501 53M1I1M1I2M1D3M1I34M on region chr4:25001557-25001563. The processing will be continued from the next cigar.
java.lang.StringIndexOutOfBoundsException: String index out of range: 111
  at java.base/java.lang.StringLatin1.charAt(StringLatin1.java:47)
  at java.base/java.lang.String.charAt(String.java:693)
  at com.astrazeneca.vardict.variations.VariationUtils.isHasAndNotEquals(VariationUtils.java:498)
  at com.astrazeneca.vardict.modules.CigarModifier.captureMisSoftly3Mismatches(CigarModifier.java:320)
  at com.astrazeneca.vardict.modules.CigarModifier.modifyCigar(CigarModifier.java:178)
  at com.astrazeneca.vardict.modules.CigarParser.parseCigar(CigarParser.java:270)
  at com.astrazeneca.vardict.modules.CigarParser.process(CigarParser.java:89)
  at java.base/java.util.concurrent.CompletableFuture.uniApplyNow(CompletableFuture.java:680)
  at java.base/java.util.concurrent.CompletableFuture.uniApplyStage(CompletableFuture.java:658)
  at java.base/java.util.concurrent.CompletableFuture.thenApply(CompletableFuture.java:2094)
  at com.astrazeneca.vardict.modes.AbstractMode.pipeline(AbstractMode.java:48)
  at com.astrazeneca.vardict.modes.SimpleMode.processBamInPipeline(SimpleMode.java:103)
  at com.astrazeneca.vardict.modes.SimpleMode.access$000(SimpleMode.java:29)
  at com.astrazeneca.vardict.modes.SimpleMode$VardictWorker.call(SimpleMode.java:86)
  at com.astrazeneca.vardict.modes.SimpleMode$VardictWorker.call(SimpleMode.java:72)
  at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
  at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
  at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  at java.base/java.lang.Thread.run(Thread.java:834)

Similar exceptions are repeated until we finally get:

VarDictJava fails (there were 11 continued exceptions during the run).
Critical exception occurs on region: chr4:25001557-25001563, program will be stopped.
java.util.concurrent.CompletionException: java.lang.RuntimeException: java.lang.IllegalArgumentException: Malformed CIGAR string: 68M1I-8M1I50M
  at java.base/java.util.concurrent.CompletableFuture.encodeThrowable(CompletableFuture.java:314)
  at java.base/java.util.concurrent.CompletableFuture.uniApplyNow(CompletableFuture.java:683)
  at java.base/java.util.concurrent.CompletableFuture.uniApplyStage(CompletableFuture.java:658)
  at java.base/java.util.concurrent.CompletableFuture.thenApply(CompletableFuture.java:2094)
  at com.astrazeneca.vardict.modes.AbstractMode.pipeline(AbstractMode.java:48)
  at com.astrazeneca.vardict.modes.SimpleMode.processBamInPipeline(SimpleMode.java:103)
  at com.astrazeneca.vardict.modes.SimpleMode.access$000(SimpleMode.java:29)
  at com.astrazeneca.vardict.modes.SimpleMode$VardictWorker.call(SimpleMode.java:86)
  at com.astrazeneca.vardict.modes.SimpleMode$VardictWorker.call(SimpleMode.java:72)
  at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
  at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1128)
  at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:628)
  at java.base/java.lang.Thread.run(Thread.java:834)

Using VarDict version 1.8.3 instead of the current 1.6.0 seems to fix the problem.

Change History (1)

comment:1 by Nicklas Nordborg, 11 months ago

Resolution: fixed
Status: newclosed

In 7067:

Fixes #1469: Update VarDict to version 1.8.3

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