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fritzsedlazeck / SURVIVOR

Toolset for SV simulation, comparison and filtering
MIT License
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SURVIVOR merge #123

Closed Caro-Ca closed 4 years ago

Caro-Ca commented 4 years ago

Hi fritzsedlazeck, I am trying to merge vcf files allocated in the same folder with only vcf files. The code used is: /home/silviav/SURVIVOR/Debug/SURVIVOR merge /hosts/linuxhome/chaperone/silviav/reads/YPS128/SRA/McClintock/sacCer2/SRR4074383.1_paired_R1/results/VCF 500 2 1 0 0 20 SV_all.vcf and the stdout message is: 

terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
Aborted (core dumped)

The parameter represented for Disabled I didn't know what to introduce so I just basically assigned it to a 0.

Hope you could help me find the problem. Thank you for your time.

fritzsedlazeck commented 4 years ago

Dear @Caro-Ca SURVIVOR requires a file that includes the paths and names to the vcf files. https://github.com/fritzsedlazeck/SURVIVOR/wiki#consensus-calling-or-comparing-svs-across-samples

Yeah the disabled was a relict but I didn't want to change the interface as I know people have integrated SURVIVOR in their pipelines.

Cheers Fritz