Abdelrahman Hosny - 2016-08-23

I have completed step 1

In step 2, I used:
java -jar tumorgenomsim_1.3.1.jar -v chrom_length/chrom_lengths_hg19.txt -n chr1.fa -k rmsk.txt -i output/normal_snvindelsim.vcf -o output/

and got the following error:
nbalaced Translocation: 5 108797309 9 27340649
Writing out B allele frequency file ......
Exception in thread "main" java.lang.ArrayIndexOutOfBoundsException: 9
at org.rpci.utility.OutputFileWriter.convertVCFtoSNV(OutputFileWriter.java:485)
at org.rpci.utility.OutputFileWriter.writeBafFile(OutputFileWriter.java:130)
at org.rpci.SVSimulation.MainSimulator.transWrite(MainSimulator.java:313)
at org.rpci.SVSimulation.MainSimulator.main(MainSimulator.java:569)

What is wrong in this?