Pe overlap consolidation

[Psy-Fer]

--peOverlapNbasesMin mate-overlap merge-and-realign — consolidated + STAR-faithful filter stage (closes #119)

Consolidates BenjaminDEMAILLE's PE mate-overlap PR, with the review-flagged filter-stage divergence from real STAR fixed and the feature validated against STAR 2.7.11b on 10k yeast pairs.

When a fragment is shorter than mate1_len + mate2_len, the mates overlap in genome space. STAR (peOverlapMergeMap) merges them into one contiguous single-end read, aligns that, and converts the result back to a two-mate pair — often stitching cleanly across the overlap where separate-mate alignment fails.

Closes #119.

Fix: merged-read find must be filter-free (defer to the PE stage)

The port aligned the merged read with the full SE driver (align_read), which applies mappedFilter's read-length gates — outFilterMatchNminOverLread (default 0.66) and outFilterScoreMinOverLread — against the merged length. STAR's peMergeRA->mapOneRead() is a find step: it locates windows without those gates, converts every candidate to PE, and runs multMapSelect()/mappedFilter() only afterward at the PE level, on the reconstructed pair (ReadAlign_oneRead.cpp:87-91). Applying the SE gate to the longer merged read silently dropped merges the PE stage would keep.

Fixed: the merged-read find now runs with the length-relative gates disabled; the existing PE decision tree (filter_paired_transcripts, which already applies the combined-length match/score gates) does the real filtering after convert_merged_transcript_to_pe.

Validation (yeast PE, --peOverlapNbasesMin 10, vs STAR 2.7.11b)

	both-mapped
peOverlap off (baseline)	rustar 8390 = STAR 8390 (exact, unchanged)
peOverlap on — before fix	rustar 8726 vs STAR 8812 → 86 pairs under-rescued
peOverlap on — after fix	rustar 8823, STAR 8812

After the fix rustar is a strict superset of STAR's peOverlap rescues: 0 pairs mapped by STAR but not rustar, plus 11 extra — all verified legitimate (proper pairs, FLAG 99/147, nM 0–1) that STAR's peMerge heuristic misses, consistent with rustar's already-documented PE-improvement cases. CIGAR agreement 17367/17624 (98.5%).

Tests

• New convert_reverse_strand_flips_mates_and_swaps_coords unit test — the review-flagged untested path: the reverse-strand m_sta = Lread − readLen − m_sta coordinate swap + the mate-strand flip (mate1 takes the fragment strand, mate2 the opposite). Asserts the strand flip, per-mate coverage, and the mirrored genomic spans.
• Spliced / exon-split conversion paths are exercised end-to-end by the yeast run (e.g. a spliced merge in ERR12389696.16897393).

Gate: 574 tests pass · clippy --all-targets 0 warnings · fmt clean. --peOverlapNbasesMin defaults to 0 (off), so the default path is unchanged.