Update CLI for variant calling

[jnalanko]

Note: this does not depend on the kbo crate at crates.io, but at the relative path "../kbo". The commit at kbo should be 11ce0663560f97b33bc77cda90f9f2eabb62ff08.

[tmaklin]

tnx!

Some changes made by me:

• Rename call-variants to call.
• Implement .vcf writer using noodles_vcf, custom implementation had some small formatting issues which weren't compatible with other tools plus I prefer to handle i/o outside of the core library so it fits better here.
• Swap role of reference and query (reference should be the seq that remains the same in the output if we run multiple queries). This could also be changed in the kbo core lib.
• Allow references (formerly queries) with more than 1 contig, these are processed separately and reported separately in the .vcf. The first column in output .vcf contains the contig name.
• Take query file as a positional argument, similar to other commands. Still errors if more than one query is supplied since this is not supported by the .vcf format.
• Increased default k to 51 since 31 seems to miss some variants and the runtime difference is not too bad.

Can be merged after the kbo core library is updated, TODO update this in Cargo.toml.