Avoid unaligned packed index accesses#2697
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Summary
PackedArraywith fixed-sizememcpyoperations.Problem
STAR intentionally packs arrays at byte-granular offsets, but several accessors cast those addresses to
uint64_t*oruint128*and dereference them. These operations are undefined on unaligned addresses and are reported during both index generation and mapping by UBSan.Validation
extras/tests/scripts/testPackedArray.shpasses; its odd-address case reports a misaligned access against unmodified 2.7.11b.genomeGeneratecompletes withUBSAN_OPTIONS=halt_on_error=1.Genome,SA,SAindex, chromosome metadata, gene/transcript/exon tables, and SJDB files, are byte-identical to unmodified 2.7.11b.