xa2multi.pl: reverse sequence and phred if orientations differ between primary and secondary alignment#5
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… alignment has different orientation than primary alignment
lh3
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xa2multi.pl: reverse sequence and phred if orientations differ between primary and secondary alignment
teepean
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lh3#5 real) Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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…, bit-exact Restructure bwa-aln-gpu into a producer/consumer pipeline: the main thread owns the GPU (read -> MT preprocess -> upload -> kernel -> download has_hit, serial on one stream so the shared per-warp global backing is never raced); each chunk is handed to ONE in-order finisher thread doing the CPU reconcile + output (.sai or fused samse), concurrent with the next chunk's GPU work. A single ordered consumer preserves drand48 (repeat-hit) and output order -> bit-exact. Structured multi-GPU-ready (replicate the GPU stage per device + round-robin chunks; keep one ordered finisher) for when a 2nd card is added. Full file (3.95M reads, fused alnse SAM): 174.2 s -> 160.9 s = 24,541 reads/s (overlap hid ~13s of the ~18s CPU tail), records BIT-EXACT (md5 e2a6e1c9). Both modes re-verified bit-exact under the pipeline (.sai eecf35c1, SAM records identical). vs CPU bwa aln -t16 + samse = 895 s -> ~5.56x end-to-end. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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When a secondary alignment given in an XA tag differs in orientation from the primary one, the xa2multi.pl now gives the reverse complementary sequence and the reverse phred string.