Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 0

[mjafin]

Hi there,
I'm calling variants in hg38 and am getting this error:

Exception in thread "main" java.lang.StringIndexOutOfBoundsException: String index out of range: 0
        at java.lang.String.charAt(String.java:658)
        at com.astrazeneca.vardict.VarDict.varType(VarDict.java:5905)
        at com.astrazeneca.vardict.VarDict.vardict(VarDict.java:966)
        at com.astrazeneca.vardict.VarDict.vardictNotParallel(VarDict.java:305)
        at com.astrazeneca.vardict.VarDict.nonAmpVardict(VarDict.java:257)
        at com.astrazeneca.vardict.VarDict.start(VarDict.java:68)
        at com.astrazeneca.vardict.Main.run(Main.java:134)
        at com.astrazeneca.vardict.Main.main(Main.java:25)
' returned non-zero exit status 1

This is in the chrUn_GL000216v2 contig that is fairly short (0-176608). I can provide you the data via Box again when you have time to pick this up.

Thanks,
Miika

[chapmanb]

Miika;
It sounds like this might be the same as the issue in this PR: #19 It's a small fix but hadn't gotten pulled into main and a release yet, as far as I know.

[mjafin]

Brad, thanks, well spotted! I'll flag these up with EPAM and will follow up properly

[mjafin]

This issue seems to have been solved now, thanks! I'll reopen if I come across it again.