Fix sjA/sjFilter/sjChunks memory leaks#2676
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- these were allocated and only used locally but not deleted Only reserve and populate `P.sjAll` vectors when Solo SJ feature is requested - reduces memory use when Solo SJ feature is not requested
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Bug fixes from upstream STAR PRs: - PR alexdobin#2163: Remove OOB write in sjdbInsertJunctions.cpp (SA.writePacked at index nSA is one past the end; memory corruption confirmed by Valgrind) - PR alexdobin#2676: Fix memory leaks in outputSJ.cpp (sjA, sjFilter, sjChunks arrays allocated but never freed) - PR alexdobin#535: Fix segfault in SA lookup shortcut in ReadAlign_maxMappableLength2strands.cpp (unreliable shortcut caused unsigned underflow and SIGSEGV on certain genomes) Performance optimizations: - PR alexdobin#791: PackedArray bitmask optimization (replace expensive double-shift with single AND in hot operator[]; ~1-2% improvement) - PR alexdobin#791: Add FastResetVector.h (O(modified) reset instead of O(N) memset; available for winBin array optimization) - PR alexdobin#773 (partial): Early rejection in stitchWindowAligns.cpp to skip unnecessary Transcript copies when alignment will obviously fail HTSlib upgrade evaluated and deferred: current 1.3 has minimal security surface (no CRAM, no network I/O, trusted input only). Note: uniquely mapped count changes slightly due to PR alexdobin#535 fix — the buggy shortcut was incorrectly skipping valid alignments. Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>
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Only reserve and populate
P.sjAllvectors when Solo SJ feature is requested