Opened 2 months ago

Closed 2 months ago

Last modified 2 months ago

#1328 closed defect (fixed)

Index out of bounds exception

Reported by: Nicklas Nordborg Owned by: Nicklas Nordborg
Priority: major Milestone: Variant Search v1.3
Component: net.sf.basedb.varsearch Keywords:
Cc:

Description

For some VCF files I get an error message when trying to view the details:

java.lang.ArrayIndexOutOfBoundsException: Index 1 out of bounds for length 1
  at net.sf.basedb.varsearch.vcf.VcfParser$VcfLine.parseFormat(VcfParser.java:297)
  at net.sf.basedb.varsearch.vcf.VcfParser$VcfLine.<init>(VcfParser.java:208)
  at net.sf.basedb.varsearch.vcf.VcfParser.nextLine(VcfParser.java:90)
  at net.sf.basedb.varsearch.vcf.VcfParser.parseToLine(VcfParser.java:105)
....

The main suspect is an entry with only a single value in the AD tag (eg. 37 instead of 37,0).

Change History (2)

comment:1 Changed 2 months ago by Nicklas Nordborg

Resolution: fixed
Status: newclosed

In 6404:

Fixes #1328: Index out of bounds exception

comment:2 Changed 2 months ago by Nicklas Nordborg

Milestone: Variant Search extension v1.3Variant Search v1.3

Milestone renamed

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