[jayhesselberth]

Closes #4

Most of #4 already landed in #3 (-1/-2, --interleaved, paired uBAM, joint pair scoring on the existing score rows for CPU and GPU, pair-aware chunking, proper-pair flags, MC, --sort coordinate, --secondary). This PR closes the remaining gaps against the issue.

Changes

• --pair-orientation fr|rf|ff (default fr), carried as PairOrientation in PairOptions. fr is the existing behaviour. rf: opposite strands, reverse mate starts at or before the forward mate. ff: same strand, mate 1 upstream.
• MQ (mate MAPQ) is now written next to MC. MC:Z:* is written when the mate is unmapped, as samtools fixmate does.
• TLEN now follows samtools fixmate (partner 5' end minus own 5' end) so a fixmate round trip is a no-op. It is identical to the old span for ordinary FR pairs, and differs for same-strand and overhanging pairs.
• Discordant pairs (mates whose best references differ, each reported at its own) are counted in the run summary.
• A non-adjacent paired BAM says to run samtools collate / samtools sort -n.
• Tests: expected names from the issue in align_paired.rs (renamed or split from the existing ones), plus joint_score_breaks_tie_a_mate_cannot, discordant_pair_flags_and_counts, non_adjacent_bam_mates_say_to_collate, pair_orientation_ff_makes_same_strand_pair_proper, and library orientation_rf_and_ff. The single-end golden test moved from align_unpaired.rs to align_paired::single_end_output_unchanged (golden file untouched, so single-end output is byte-identical). Fixture: one extra discordant pair appended to the synthesized pairs files (gen_pair_fixture.py, no real data).

How the equality tests were checked to fail

Each was run against a deliberately broken implementation and failed, then the break was reverted:

Test	Breakage
joint_score_breaks_tie_a_mate_cannot	pair score = mate 1 only
fastq_pair_matches_interleaved_and_ubam	interleaved reader drops mate-1 qualities
sort_coordinate_matches_samtools_and_fixmate	TLEN off by one
single_end_output_unchanged	unique MAPQ 59
discordant_pair_flags_and_counts	discordant counter not incremented
mate_name_mismatch_is_an_error	name check disabled
orientation_rf_and_ff	ff geometry always true

device_gpu_output_is_byte_identical compiles under --features gpu (clippy clean) but was not run: no GPU here.

Checks

cargo fmt --all --check, cargo clippy --workspace --all-targets -- -D warnings (also with --features gpu), cargo nextest run --workspace (126 passed), cargo test --doc --workspace.

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