Handling of symbolic alleles

[vruano]

I got a Java exception when processing a VCF that has a single variant record whose alt allele is not the usual base sequence but a symbolic allele (<DUP> to be more precise)

Although there is a obvious work around (remove such entries before calling haplogrep) I think the tool should simply ignore them on the fly.

The exception is thrown from within a dependency (haplogrep-core) class importer.VcfImporter

Cannot share input due to privacy concerns however I think that a simple vcf that contains such a symbolic alleles should trigger it.

Version:
the latest: v3.2.2
Exception (and only stderr output):

java.lang.StringIndexOutOfBoundsException: String index out of range: 0
        at java.base/java.lang.StringLatin1.charAt(StringLatin1.java:47)
        at java.base/java.lang.String.charAt(String.java:693)
        at importer.VcfImporter.load(VcfImporter.java:215)
        at genepi.haplogrep3.haplogrep.io.readers.impl.VcfInputFileReader.read(VcfInputFileReader.java:39)
        at genepi.haplogrep3.haplogrep.io.readers.InputFileReaderFactory.read(InputFileReaderFactory.java:33)
        at genepi.haplogrep3.tasks.ClassificationTask.run(ClassificationTask.java:90)
        at genepi.haplogrep3.commands.ClassifyCommand.call(ClassifyCommand.java:96)
        at genepi.haplogrep3.commands.ClassifyCommand.call(ClassifyCommand.java:22)
        at picocli.CommandLine.executeUserObject(CommandLine.java:1783)
        at picocli.CommandLine.access$900(CommandLine.java:145)
        at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2150)
        at picocli.CommandLine$RunLast.handle(CommandLine.java:2144)
        at picocli.CommandLine$RunLast.handle(CommandLine.java:2108)
        at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:1975)
        at picocli.CommandLine.execute(CommandLine.java:1904)
        at genepi.haplogrep3.App.main(App.java:131)