Use flat arrays in p7_Builder_MaxLength - #23
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kevinmoran1988 wants to merge 1 commit into
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kevinmoran1988 wants to merge 1 commit into
kevinmoran1988 wants to merge 1 commit into
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Replace per-state 2-element row allocations with flat columns, widen transitions to double once, and carry the current column's M[k-1] and D[k-1] in locals. Same operations in the same order. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
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p7_Builder_MaxLength() kept its two DP columns as 3(M+1) separately allocated 2-element rows, and re-read hmm->t[k] and recomputed (1 - t) inside the inner loop. This uses flat columns, widens the transitions to double once, and carries the current column's M[k-1] and D[k-1] in locals so the D recurrence no longer goes through memory. The operations and their order are unchanged, so max_length is identical.
bathbuild over 5232 dipteraODB12 alignments, serial, 3 runs each, in seconds:
base 230.97 / 232.23 / 229.27
patch 224.01 / 226.81 / 224.33 (1.03x)
Output byte-identical to base on that corpus.
🤖 Generated with Claude Code