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mkirsche / Jasmine

Jasmine: SV Merging Across Samples
MIT License
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Problem with --output_genotypes parameter #8

Closed mldmort closed 3 years ago

mldmort commented 3 years ago

Hi,

I've noticed that when I'm running Jasmine with parameter: --output_genotypes I get an error as following:

Exception in thread "main" java.lang.NullPointerException
    at AddGenotypes.addGenotypes(AddGenotypes.java:150)
    at PipelineManager.addGenotypes(PipelineManager.java:191)
    at Main.postprocess(Main.java:91)
    at Main.main(Main.java:27)

And Jasmine does not finish the job, and writes just part of the calls in the output file. Without --output_genotypes Jasmine doesn't have any problems and finishes, but doesn't output genotypes in the merged output VCF file.

I only have these genotypes in my VCF files (generated by Sniffles):

0/0
0/1
1/1

Any idea what can be the problem? Thanks,

mkirsche commented 3 years ago

I think you accidentally opened this issue twice at the same time, so I'm going to go ahead and close this one and point to https://github.com/mkirsche/Jasmine/issues/9