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NPE when annotating Delly2 files #88

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holtgrewe opened this issue Dec 30, 2022 · 1 comment · Fixed by #89
Closed

NPE when annotating Delly2 files #88

holtgrewe opened this issue Dec 30, 2022 · 1 comment · Fixed by #89
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Exception in thread "main" java.lang.NullPointerException
        at com.github.bihealth.varfish_annotator.annotate_svs.AnnotateSvsVcf.mergeChromRecords(AnnotateSvsVcf.java:348)
        at com.github.bihealth.varfish_annotator.annotate_svs.AnnotateSvsVcf.mergeSortedGts(AnnotateSvsVcf.java:278)
        at com.github.bihealth.varfish_annotator.annotate_svs.AnnotateSvsVcf.run(AnnotateSvsVcf.java:210)
        at com.github.bihealth.varfish_annotator.VarfishAnnotatorCli.main(VarfishAnnotatorCli.java:72)
@holtgrewe holtgrewe added the bug Something isn't working label Dec 30, 2022
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holtgrewe commented Dec 30, 2022 •
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Root Cause Analysis
Delly2 writes out the INFO/SVMETHOD tag whose value is EMBL.DELLY while we use DELLY2_SV internally to differentiate from Delly2 CNV.

holtgrewe added a commit that referenced this issue Dec 30, 2022
@holtgrewe
Fix problem when annotating Delly2 VCF files (#88)
6d37581 
Closes: #88
Related-Issue: #88
Projected-Results-Impact: none
@holtgrewe holtgrewe linked a pull request Dec 30, 2022 that will close this issue
fix: Delly2 VCF files work now when merging SV VCF files (#88) #89
Merged
holtgrewe added a commit that referenced this issue Dec 30, 2022
@holtgrewe
Fix problem when annotating Delly2 VCF files (#88)
05a301f 
Closes: #88
Related-Issue: #88
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Dec 30, 2022
@holtgrewe
Fix problem when annotating Delly2 VCF files (#88)
b576aab 
Closes: #88
Related-Issue: #88
Projected-Results-Impact: none
holtgrewe added a commit that referenced this issue Dec 30, 2022
@holtgrewe
Fix problem when annotating Delly2 VCF files (#88)
a564569 
Closes: #88
Related-Issue: #88
Projected-Results-Impact: none
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fix: Delly2 VCF files work now when merging SV VCF files (#88) varfish-org/varfish-annotator
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