If `-o` is set to the same thing as the input VCF, hap.py will over-write the input

[ifiddes-10x-zz]

In other words, if you have a query VCF in the form my.vcf.gz, and you set -o my, your my.vcf.gz will be silently over-written on completion.

It seems also that the over-written version will have a new header with chr in the CONTIG= tags, which breaks subsequent runs.

Maybe it is worth warning the user that they are going to clobber their inputs in this case?

[ifiddes-10x-zz]

Also this is what caused the errors I reported in issue #40. The header, and particularly the CONTIG tags, is broken for subsequent runs.