Add --compression-level option for VCF/BCF output

[tfenne]

Motivation

GLIMPSE2_phase, GLIMPSE2_ligate, and GLIMPSE2_concordance hardcode the htslib
output mode to compressed BCF ("wb") / compressed VCF ("wz"), so there is no way
to change the compression level or to emit an uncompressed BCF. Every run pays full
(level-6) compression cost, which is wasteful for large intermediate files that the
next pipeline stage immediately re-reads and decompresses.

@srubinacci this is a purely mechanical change in the output compression/writing layer, so hopefully can be reviewed (and merged) even without the ability to benchmark on UKB?

Change

Adds a --compression-level option (INT, default 6, range 0–9) to all three tools,
mirroring bcftools -l/--compression-level so the semantics are familiar:

• The level is appended to the htslib mode string only for compressed formats
  (wb/wz); plain uncompressed VCF (.vcf) is left untouched.
• Level 0 yields a BGZF-stored (uncompressed) BCF — still BGZF-framed and
  indexable, just not deflated — equivalent to bcftools -l 0.
• The default of 6 matches htslib's implicit default, so output is byte-identical
  when the flag is unused.

Tool	Output affected
phase	main VCF/BCF output (BGEN path unaffected — it has its own --bgen-compr)
ligate	ligated VCF/BCF output
concordance	_rej_sites.bcf / _conc_sites.bcf / _disc_sites.bcf diagnostic outputs

Help text, startup logging, and the per-tool documentation tables are updated for all
three tools.

Testing

• All three tools build cleanly.
• Out-of-range values (e.g. --compression-level 12) are rejected with a clear error.
• Level 0 produces an uncompressed BCF matching bcftools -Ob0; higher levels compress;
  decoded records are identical across levels.
• Verified byte-identical default output against current master (matching MD5).
• ligate's inline CSI index at level 0 verified usable (region query + bcftools index -s).

[srubinacci]

Thanks! Yes, very easy to add. I should be able to test this very quickly (no need for UKB)