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seppinho / haplogrep-cmd

HaploGrep - mtDNA haplogroup classification. Supporting rCRS and RSRS.
https://haplogrep.i-med.ac.at/
MIT License
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Haplogrep error with a vcf-merge file. #45

Open VGDEC opened 3 years ago

VGDEC commented 3 years ago

Hi, I have created a merged vcf file using vcf-merge tool for ~1000 samples. When I am trying to provide this file as an input for the haplogrep, it is showing the following error:

Start Classification... java.lang.NumberFormatException: For input string: "." at sun.misc.FloatingDecimal.readJavaFormatString(FloatingDecimal.java:2043) at sun.misc.FloatingDecimal.parseDouble(FloatingDecimal.java:110) at java.lang.Double.parseDouble(Double.java:538) at java.lang.Double.valueOf(Double.java:502) at importer.VcfImporter.load(VcfImporter.java:205) at genepi.commands.HaplogrepCommand.call(HaplogrepCommand.java:156) at genepi.commands.HaplogrepCommand.call(HaplogrepCommand.java:20) at picocli.CommandLine.executeUserObject(CommandLine.java:1953) at picocli.CommandLine.access$1300(CommandLine.java:145) at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2352) at picocli.CommandLine$RunLast.handle(CommandLine.java:2346) at picocli.CommandLine$RunLast.handle(CommandLine.java:2311) at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) at picocli.CommandLine.execute(CommandLine.java:2078) at genepi.App.main(App.java:59)

Kindly, please suggest what should be done.

seppinho commented 2 years ago

Thanks, can you provide a minimal input file? Looks like there is a variant included in the file with an AF of ".". (We currently allow an AF of > 0.0).