ClairS crashing with spaces in input file name

[RenzoTale88]

ClairS crashing with spaces in input file name

[RenzoTale88]

@zhengzhenxian thanks for the quick reply. Unfortunately, the issue is not always this easy to sort out: it is fairly common for users to have spaces in their user names, which in turn makes their home the folder having space in it. This would make the issue impossible to circumnvent for these users. I appreciate the complexity of fixing this though!

[zhengzhenxian]

@RenzoTale88 Thanks for raising this. The space in the input path leads to parser error. We have tried to add path quotation but find it hard to cover all the parameters and especially for the softwares we are using, such as Clair3, WhatsHap, and LongPhase.

We would suggest you remove the space in all your input parameters, including the input path of BAM, REF, BED, and genotyped VCF.