Segfaults with some VCF files - Githubissues

fritzsedlazeck / SURVIVOR_ant

A framework to annotate SVs with previous known SVs (vcf file) and or with genomic features (gff and or bed files)

MIT License

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Segfaults with some VCF files #8

Open dustinbleile opened 6 years ago

dustinbleile commented 6 years ago

In attempting to use SURVIVOR_ant, we encountered segfaults when using VCFs from DELLY, Breakseq or MetaSV. The manta VCF files appear to be handled correctly.

The command below will segfault: survivor_ant-core-0.1.0 -i DELLY_combined.vcf -v metasv.vcf,diploid_manta.vcf,somatic_manta.vcf -o colo_test.vcf

The problem appears to be in TNode.h::add called by IntervallTree::add_vcf

VCF files: (Added .txt extension to VCF files to allow upload)

DELLY_combined.vcf.txt metasv.vcf.txt diploid_manta.vcf.txt somatic_manta.vcf.txt

fritzsedlazeck commented 6 years ago

Hi thanks for reporting this. SURVIVOR_ant is sadly still in an inmatured state. What are you trying todo? Merge/ compare VCF SVs files? Please check out SURVIVOR ( SURVIVOR ) option: merge to do that.

Thanks Fritz