seppinho/mutserve

Indels in VCF

haansi opened this issue · 1 comments

haansi commented

Indel: true
Write VCF: true

Exception in thread "main" java.lang.NumberFormatException: For input string: "311.1"
	at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
	at java.lang.Integer.parseInt(Integer.java:580)
	at java.lang.Integer.parseInt(Integer.java:615)
	at genepi.io.table.reader.AbstractTableReader.getInteger(AbstractTableReader.java:49)
	at genepi.io.table.reader.AbstractTableReader.getInteger(AbstractTableReader.java:29)
	at genepi.mut.util.MutationServerReader.parse(MutationServerReader.java:38)
	at genepi.mut.util.MutationServerReader.parse(MutationServerReader.java:18)
	at genepi.mut.util.VcfWriter.createVCF(VcfWriter.java:40)
	at genepi.mut.pileup.PileupToolLocal.run(PileupToolLocal.java:236)
	at genepi.base.Tool.start(Tool.java:193)
	at genepi.base.Toolbox.start(Toolbox.java:44)
	at genepi.mut.Server.main(Server.java:42)
seppinho commented

Indels still excluded but no null pointer anymoer