fix(transcriptome-bam): populate mate fields on paired-end records

[pinin4fjords]

Summary

Paired-end records in Aligned.toTranscriptome.out.bam were missing every mate field: no PROPERLY_SEGMENTED (0x2) flag, no MATE_REVERSE_COMPLEMENTED (0x20), RNEXT=*, PNEXT=0, TLEN=0. Salmon's alignment-mode fragment-length inference reads these fields; with them missing it falls back to its default prior (mean=250, sd=25) and EffectiveLength for short transcripts gets over-shrunk, inflating their TPMs.

samtools flagstat pre-fix: 0 / 77 300 properly-paired records. STAR on the same data: 78 886 / 78 886.

Fix

In build_transcriptome_records_pe, after the existing flag-stamping loops and before the interleave, walk the projected (rec1, rec2) pairs alongside their (p1, p2) transcripts and stamp:

• PROPERLY_SEGMENTED on both (concordance is guaranteed at this point - both mates project to the same transcript by construction).
• MATE_REVERSE_COMPLEMENTED mirroring the other mate's REVERSE_COMPLEMENTED.
• mate_reference_sequence_id and mate_alignment_start from the other projection.
• template_length with STAR's sign convention: magnitude max(end1,end2) - min(start1,start2) + 1, leftmost mate positive, rightmost negative.

Mirrors the genome-space build_paired_mate_record (which already does all of this) so the transcriptome path is now byte-symmetric for shared fields. The TLEN-signing logic is the same calculate_insert_size helper the genome path uses (lifted to pub(crate)); the mate-bookkeeping itself is factored into a new apply_pe_transcriptome_mate_fields helper in src/io/sam.rs so it can be unit-tested in isolation.

Test plan

• New unit tests assert PROPERLY_SEGMENTED, populated mate ref id, non-zero signed TLEN (forward and reverse cluster cases)
• Existing transcriptome tests pass
• cargo build
• cargo clippy --lib -- -D warnings
• cargo fmt --check

After the fix, samtools view -c -f 2 <transcriptome.bam> returns the count of primary paired records (not 0).

Fixes #22

[pinin4fjords]

Verified end-to-end on macOS/aarch64 against the rebuilt fix branch with the issue's exact reproducer (PE yeast + --quantMode TranscriptomeSAM --quantTranscriptomeSAMoutput BanSingleEnd).

$ samtools flagstat <transcriptome.bam>
77300 + 0 in total (QC-passed reads + QC-failed reads)
68408 + 0 primary
68408 + 0 paired in sequencing
34204 + 0 read1
34204 + 0 read2
68408 + 0 properly paired (100.00% : N/A)

First record pair SRR6357072.7414694 on YAR009C:

FLAG=83   POS=847   RNEXT==  PNEXT=776  TLEN=-172
FLAG=163  POS=776   RNEXT==  PNEXT=847  TLEN=+172

• FLAG 83 / 163 both carry 0x2 (PROPERLY_SEGMENTED)
• RNEXT = matches
• PNEXT populated from the mate's POS
• TLEN signed correctly (leftmost mate at POS 776 gets +172, rightmost gets −172)

Pre-fix the same invocation produced 0 / 73172 properly-paired records and every record had RNEXT=* PNEXT=0 TLEN=0. LGTM.