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Exception in thread "main" java.lang.NumberFormatException: For input string: "21.44" #93

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Nicolai-vKuegelgen opened this issue Jan 16, 2023 · 0 comments · Fixed by #94
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Exception in thread "main" java.lang.NumberFormatException: For input string: "21.44" #93

Nicolai-vKuegelgen opened this issue Jan 16, 2023 · 0 comments · Fixed by #94
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@Nicolai-vKuegelgen
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Describe the bug
The GQ/SQ field from DRAGEN does not contain integer values but floats. Subsequently one gets the exception

Now on contig MT
Exception in thread "main" java.lang.NumberFormatException: For input string: "21.44"
        at java.lang.NumberFormatException.forInputString(NumberFormatException.java:65)
        at java.lang.Integer.parseInt(Integer.java:580)
        at java.lang.Integer.parseInt(Integer.java:615)
        at com.github.bihealth.varfish_annotator.annotate.AnnotateVcf.buildGenotypeValue(AnnotateVcf.java:833)
        at com.github.bihealth.varfish_annotator.annotate.AnnotateVcf.constructOutputRecord(AnnotateVcf.java:523)
        at com.github.bihealth.varfish_annotator.annotate.AnnotateVcf.writeOutputRecords(AnnotateVcf.java:442)
        at com.github.bihealth.varfish_annotator.annotate.AnnotateVcf.annotateVariantContext(AnnotateVcf.java:335)
        at com.github.bihealth.varfish_annotator.annotate.AnnotateVcf.annotateVcf(AnnotateVcf.java:206)
        at com.github.bihealth.varfish_annotator.annotate.AnnotateVcf.run(AnnotateVcf.java:119)
        at com.github.bihealth.varfish_annotator.VarfishAnnotatorCli.main(VarfishAnnotatorCli.java:64)

To Reproduce
Steps to reproduce the behavior:

  1. Annotate any file from DRAGEN on chrMT

Expected behavior
Parse as float and maybe convert to int.
@Nicolai-vKuegelgen Nicolai-vKuegelgen added the bug Something isn't working label Jan 16, 2023
holtgrewe added a commit that referenced this issue Jan 16, 2023
@holtgrewe
Interpret FORMAT/SQ as Float (#93)
62aab01
@holtgrewe holtgrewe linked a pull request Jan 16, 2023 that will close this issue
Interpret FORMAT/SQ as Float (#93) #94
Merged
holtgrewe added a commit that referenced this issue Jan 16, 2023
@holtgrewe
Interpret FORMAT/SQ as Float (#93)
b845e48 
Closes: #93
Related-Issue: #93
Projected-Results-Impact: none
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Interpret FORMAT/SQ as Float (#93) varfish-org/varfish-annotator
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