Potential Issues in Current Development Version

[HMU-WH]

Hi,

I encountered the following issues while using Battenberg and would like to see them addressed in future releases:

1. In prepare_wgs.R, the comments for lines L57-L59 should be restored; otherwise, it will cause errors in the loci matching step, as described in 'chr' removing added back and java version #160 .
2. In the combine.impute.output() method, the write.table() should use sep = "\t" instead of sep = " ". Otherwise, when usebeagle = FALSE, it will cause read_imputed_output() to fail to read the file correctly.
3. The chromosome names in the <Chromosome>.1kg.phase3.v5a_GRCh38nounref.vcf.gz files, located within the beagle_chr.zip archive of Battenberg_reference_hg38.zip, are missing the "chr" prefix. If users do not detect this issue promptly, it will lead to runtime errors.

Looking forward to seeing Battenberg get even better.