Initialize optional transcriptome state

[justinblethrow-cloud]

Summary

• Construct a valid Transcriptome object before APIs requiring a reference receive it.
• Keep soloCellFiltering on its early-exit path with a real local transcriptome object.
• Reuse the main transcriptome object for final Solo processing.
• Initialize Transcript::sjYes in reset().
• Add a focused initialization regression test.

Problem

Ordinary mapping currently forms Transcriptome& references from a null pointer in STAR.cpp, even when downstream code does not inspect transcriptome data. UBSan reports those reference bindings. Separately, Transcript::sjYes is left uninitialized and can be read during alignment; UBSan reports an invalid bool value.

The Transcriptome constructor already returns immediately when transcriptome quantification is not requested, so constructing a valid no-op object preserves the existing fast path.

Validation

• extras/tests/scripts/testTranscriptInitialization.sh passes; the same placement-new test against unmodified 2.7.11b reports an invalid bool load.
• A full ASan/UBSan build succeeds.
• Ordinary mapping no longer reports null-reference or invalid-bool diagnostics.
• SAM records are byte-identical to unmodified 2.7.11b.