add support for Number=R fields when trimming alleles

- Number=R for INFO and FORMAT introduced in VCF4.2
- when removing alleles, removed appropriate entries from R fields
- use the new api in a few places
Allow overriding default columns indexes in bcf_sr_regions_init
vcf: new function bcf_remove_filter()
Merge branch 'develop' into bcftools+calling
Merge branch 'bcftools+calling' into develop