fix: correct _is_phased() early return and prevent KeyError on duplicate variants

[haoyu-haoyu]

Summary

Two bugs fixed in preprocessor/pcat/utilities.py:

1. _is_phased() returns on first sample (line ~879)

The function checks phasing status but returns immediately on the first GT field, never examining subsequent samples.

# Before (bug): returns on first sample
for x in gt_field:
    if '/' in x:
        return False
    else:
        return True  # exits loop on first iteration!

# After (fix): checks all samples
for x in gt_field:
    if '/' in x:
        return False
return True  # only returns True after checking ALL samples

Impact: Multi-sample VCFs may have incorrect phasing determination, leading to wrong star allele calls.

2. KeyError on duplicate normalized variants (fixes #222)

ref_pos_dynamic[pos].pop(ref_alt) crashes when multiple input variants normalize to the same coordinate/allele pair. Changed to .pop(key, None) to handle collisions gracefully.

Test plan

• Run existing preprocessing tests: cd preprocessor && pytest tests/
• Test with multi-sample phased VCF to verify phasing preserved