About --chromosomes option

[ChenJuiYANG]

Hi, I have a suggestion for specifying chromosomes option.
The current version has the argument '--chromosomes' used for specifying chromosome(s). However, if the specifying chromosome is not in the vcf file, we will get an error message as:

[pixy] Checking chromosome data...Exception: ('[pixy] ERROR: the following chromosomes were specified but not occur in the VCF: ', ['chr_name'])

Can we have an option to skip this checkpoint and just ignore those non-exist chromosomes?
(I have a few subsets vcf files with a full contigs list. For parallelism, I separated contigs to small groups from the list, but not all contigs are included in all vcf files.)

And can we have an option to exclude specifying chromosomes? And maybe an option to exclude specifying region?
(For chromosome-level data, this would be handy to only process those unplaced small contigs by excluding chromosomes rather than specifying all unplaced contigs.)

Thanks.
Chen-Jui

[ksamuk]

Sure thing, that would makes sense and we can add that!