Dot Conversion to Number Error

[DarioS]

I have a VCF file which is a merge of a set of VCF files and hence some columns have all values set to ..

##source=DRAGEN_SNV
##bcftools_mergeVersion=1.16+htslib-1.16
##bcftools_mergeCommand=merge -Oz -o allGermline.vcf.gz 010_Fibro.hard-filtered.vcf.gz 090_Fibro.hard-filtered.vcf.gz ...
##bcftools_viewVersion=1.16+htslib-1.16
    ...        ...
chrM    72      .       T       C       .       PASS    MQ=208.6;FractionInformativeReads=1 ...
chrM    73      .       A       G       .       PASS    MQ=192.56;FractionInformativeReads=0.999 ...    
    ...        ...

Haplogrep 3 doesn't like it.

Haplogrep 3 3.2.1
java.lang.NumberFormatException: For input string: "."
        at java.base/jdk.internal.math.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2054)
        at java.base/jdk.internal.math.FloatingDecimal.parseDouble(FloatingDecimal.java:110)
        at java.base/java.lang.Double.parseDouble(Double.java:651)
        at java.base/java.lang.Double.valueOf(Double.java:614)
       ...        ...
        at genepi.haplogrep3.App.main(App.java:131)

Could it be more gracefully caught and ignored?

[seppinho]

Any chance you can provide a file to me?

[DarioS]

Has to be txt file suffix for GitHub to allow it: test.vcf.txt

[seppinho]

thx!

[DarioS]

Will you fix this bug soon or not?

[ramprasadn]

Hey @seppinho, I'm running into the same issue. Is there a fix for this?