[Useq-users] Errors with VCF comparator

[Ravi V. S. - Q. <Rav...@qi...>]

I am using VCFComparator from the USeq_8.7.6 package. This tool very useful in comparing with NIST GIB calls. However, there seems to be a bug in the code that is triggered by some bed files while others work fine. 

Exception in thread "main" java.lang.NegativeArraySizeException
        at edu.utah.seq.vcf.VCFParser.filterVCFRecords(VCFParser.java:325)
        at edu.utah.seq.vcf.VCFComparator.parseFilterFiles(VCFComparator.java:420)
        at edu.utah.seq.vcf.VCFComparator.<init>(VCFComparator.java:69)
        at edu.utah.seq.vcf.VCFComparator.main(VCFComparator.java:515)


In an effort to narrow the problem down, I supplied a VCF with no variant calls (but a header), and still got the error with  this bed file. I am comparing against NIST 2.18 calls. My command line:


java -jar -Xmx22g /mnt/fdkbio05/rvijaya/software/USeq_8.7.6/Apps/VCFComparator -a ~/misc/NA12878_NIST/NISTIntegratedCalls_14datasets_131103_allcall_UGHapMerge_HetHomVarPASS_VQSRv2.18_all_nouncert_excludesimplerep_excludesegdups_excludedecoy_excludeRepSeqSTRs_noCNVs.vcf -b ~/misc/NA12878_NIST/union13callableMQonlymerged_addcert_nouncert_excludesimplerep_excludesegdups_excludedecoy_excludeRepSeqSTRs_noCNVs_v2.18_2mindatasets_5minYesNoRatio.bed -c dummy.vcf -d test.bed -p NIST_comparison

Any pointers on fixing this problem? I am attaching the vcf and the bed files that I am using. 

Thanks,
Ravi