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mkirsche / Jasmine

Jasmine: SV Merging Across Samples
MIT License
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java.lang.NullPointerException #49

Open nvnieuwk opened 1 year ago

nvnieuwk commented 1 year ago

Hi, thanks for this awesome tool! I'm currently busy implementing it into my pipeline but I'm running into this error using a minimal test data:

delly_PosCon3.vcf has 3 variants
manta_PosCon3.vcf has 1 variants
whamg_PosCon3.vcf has 1 variants
Number of threads: 2
Merging graph ID: null
Merging graph ID: chr14_DEL_
Exception in thread "main" java.lang.NullPointerException
        at java.base/java.util.TreeMap.getEntry(TreeMap.java:345)
        at java.base/java.util.TreeMap.get(TreeMap.java:277)
        at ParallelMerger$MyThread.run(ParallelMerger.java:86)
        at ParallelMerger.run(ParallelMerger.java:62)
        at Main.runJasmine(Main.java:71)
        at Main.main(Main.java:22)

The commands I used are: 

$ ls *.vcf > vcfs.txt
$ jasmine \
    file_list=vcfs.txt \
    out_file=PosCon3.vcf \
    threads=2 \
    min_support=3

And the test data used is inside this folder (3 small VCF files): jasminesv.tar.gz

I hope you are able to recreate the error with this information.

Cheers, Nicolas

nvnieuwk commented 1 year ago

It seems related to the parallelization of the tool. If I run it with only one thread, the tool works fine