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
Merge branch 'develop' of git://github.com/samtools/htslib into feature/number_R
vcf: New bcf_get_info_string() wrapper
vcf: New API bcf_get_format_string()
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
vcf: fix in bcf_get_genotypes, sanity check too strict for GT
vcf: Tip to workaround missing contig tags
hts indexing: Allow arbitrary chromosomal order.

Originally, hts_idx_push required that chromosomes come
in the same order in which they appear in the header. This
requirement seems too strict, valid BCFs could not be indexed.
vcf: New bcf_hdr_id2hrec() and bcf_hrec_format() functions
vcf: New vcf_write_line() function
synced_bcf_reader: New bcf_sr_seek() function
vcf: New bcf_translate() and bcf_hdr_combine() API
idx: Support for "." queries to retrieve all records
vcf: New bcf_has_filter() API function
Fix hseek() return value test

The previous fseeko() returns 0 for success, while hseek() returns
the new stream offset.  Testing >= 0 works for both.  Fixes a bug
introduced by 6416ebf2717cbcb956692f2eeec33649a9b25ec2.
vcf: new experimental bcf_hdr_set_samples() for subsetting

Parsing of VCF is slow. When only one or few samples are needed,
bcf_read() can be 4-5x faster for VCF after bcf_hdr_set_samples()
is called, however, the penalty of this for reading BCF is ~10%.

The performance was tested with
    bcftools query -f'[%SAMPLE\t%PL\n]' <file> -s <sample>