CrossMap v0.5.4 outputs fake data when it failed to convert the data.

[monagai]

CrossMap v0.5.4 outputs fake data when it failed to convert the data.

$ CrossMap.py vcf mm39ToMm10.over.chain.gz test.vcf mm10.fa out.vcf

• mm39ToMm10.over.chain.gz: https://hgdownload.soe.ucsc.edu/goldenPath/mm39/liftOver/mm39ToMm10.over.chain.gz

• test.vcf, out.vcf, out.vcf.unmap: I attached it. test.vcf.gz out.vcf.gz out.vcf.unmap.gz

The 2nd line in test.vcf (ID=62) seems the position which cannot be converted to mm10. Ensemble cannot convert the position either. However, CrossMap returns the same data for 2nd line as 1st line in test.vcf and does not report unmapped data.