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fix: reject scorings the aligner cannot carry - #634
-A, -B, -d and -U were parsed with atoi and never range-checked, so values a user can pass abort, wrap, overflow or give different output per SIMD tier:
The match score and the negated mismatch penalty are stored in int8_t (bwa_fill_scmat, the kswv constructor, the --meth matrices). -A 128 wraps to -128, and -A 256 (or any scoring that wraps the maximum substitution score to 0) makes the mate-rescue kernel's score2 window divide by zero. -A 127 alone scales the default -B to 508, which wraps to a positive mismatch score.
A match score of 0 or less leaves nothing to align. A negative mismatch penalty scores a mismatch above zero, which breaks the 8-bit kernels' admission tests (they take -A as the largest per-base score) and the mapping-quality identity term (it divides by a + b). Measured on 200k WGS pairs on AMD Zen 4 (AVX2 and AVX-512BW, forced) and AWS Graviton 4 (NEON), clang 19.1.7, with the penalties pinned:
-A 0: SIGFPE on both x86 tiers (the score2 divide); NEON runs, with UBSan reporting the division by zero.
-A -1: AVX2 and AVX-512BW agree, NEON gives a different record set; UBSan reports a float-to-int overflow in the pairing score (mem_pair reads a negative score back from its unsigned key).
-B -4 and -B -127: all three tiers give different record sets; UBSan reports an overflow in raw_mapq.
The default scoring is byte-identical across the three tiers.
-d -1 aborts on the 8-bit banded extension's zdrop >= 0 assertion (live in release builds).
An -O + -E sum of 2^29 or more overflows int in ksw_global2, whose out-of-band cells sit at -2^30 and lose o + e twice more; -O 536870912 overflows and still exits 0.
-U near INT_MIN overflows the paired-end score - pen_unpaired.
Now:
At parse: -A must be an integer in 1..127, -B a complete int, and -d and -U non-negative ints. With -A positive, update_a's scaling keeps every sign and stays inside int (only built-in defaults are scaled; the largest product is 127 × 100).
check_effective_scoring() checks the effective values after -A scaling and the -x presets, and again after the --meth defaults: mismatch penalty in 0..128 and each gap open + extension sum ≤ 2^29 - 1. Each refusal reports the effective value and the options behind it, like the existing --meth mismatch-penalty check. With a ≥ 1 and b ≥ 0, the mapping-quality divisor a + b is at least 1. The sign checks on the gap penalties, z-drop and unpaired penalty are gone from the effective check: their parse checks plus a positive -A already guarantee them.
Decisions:
-A 0 and a negative -A are refused even with every penalty given. They used to be the contained-seed skip's proof-envelope legs in compat_contained_skip_identity.sh; those legs now check the refusal, and the envelope predicate (mem_skip_contained_ext_sound, a >= 0) gets a unit test. The driver's guard and its notice stay, unreachable from the command line.
A negative -B is refused on every path. -B 0 stays accepted off --meth (it only affects placement), and --meth keeps refusing it.
A negative -U is refused; it ran before (a bonus for leaving a pair unpaired, which the pairing code does not expect).
-A 127 alone is refused because it scales the default -B to 508; -A 127 -B 4 runs. The largest -A that runs without -B is 32.
The messages:
ERROR: -A match score must be an integer in 1..127 (got 0): a score of 0 or less leaves nothing to align, and the alignment kernels store it in 8 bits
ERROR: -B mismatch penalty must be an integer (got 4x)
ERROR: -d z-drop must be a non-negative integer in 0..2147483647 (got -1)
ERROR: -U unpaired penalty must be a non-negative integer in 0..2147483647 (got -1)
ERROR: the effective mismatch penalty is -4, outside 0..128: a negative penalty scores a mismatch above zero, which the 8-bit alignment kernels and the mapping-quality model do not allow, and the kernels store its negation in 8 bits (check -B and -A; -A scales the default -B unless -B is given)
ERROR: the effective gap open plus extension penalty is 536870912 for deletions and 7 for insertions; each must be at most 536870911 so the alignment kernels' gap scores stay in range (check -O, -E and -A)
Output change
None for any scoring that is accepted. Every newly refused scoring crashed, wrapped, overflowed or gave tier-dependent output before, except a negative -U. Documented under "Degenerate numeric inputs" in whats-different/equivalence.md, with the ranges added to the mem option reference and the usage text.
Out of scope: the kswv kernel's own guard against a zero maximum substitution score and its dead-group score2 write (#633), and -T/-L, which are not range-checked here.
Test plan
arg_range_validation.sh: refusals for -A 128/256/20000000/2x/0/-1/-128, -A 0 and -A -1 with every penalty pinned, -B 129/-1/-4/-127/4x, -A 4 -B -4, -A 33 and -A 127 (effective -B), -d -1/5x, -U -1/-2147483647/5x, and -O/-E sums one past the bound for each gap type; acceptance checks (each run must reach index loading with no scoring refusal) for defaults, -A 1/2/32, -A 127 -B 4, -B 0/128, -d 0 -U 0, -O 536870910, the three -x presets, --meth, --meth -A 2 and --meth-scoring genomic -A 32
compat_contained_skip_identity.sh: the -A -1 and -A 0 envelope legs now assert the parse refusal; test/unit/test_skip_contained_envelope.cpp pins the predicate's boundary
meth_collapsed_scoring.sh: --meth -B 0 is refused by the --meth guard, --meth -B -1 by the scoring check; the -A 0 route is gone
Host evidence for the refused scorings (above)
-fsyntax-only of src/fastmap.cpp and the new unit test; shellcheck and shfmt clean; README contract, regression coverage, shell and NDEBUG lints pass locally
CI (build, unit, regression, all tiers): 27 passed, 2 skipped by the workflow
Summary by CodeRabbit
Bug Fixes
Invalid scoring options are now rejected with an error, including out-of-range match scores, invalid effective mismatch penalties, negative z-drop or unpaired penalties, and excessive gap penalties.
The -A option accepts only values from 1 to 127; negative values and zero are rejected.
Documentation
Updated scoring-option documentation to clarify accepted ranges and how effective penalties are calculated.
Clarified the behavior of contained-seed extension when -A is below 1.
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Walkthrough
Out-of-range scoring values could cause wrapping, overflow, crashes, or SIMD-tier-dependent output. mem now validates parsed and effective scoring values and rejects invalid options. Documentation and regression tests cover the bounds and contained-seed behavior.
Changes
Scoring validation
Layer / File(s)
Summary
Parse and validate scoring options src/fastmap.cpp
mem validates -A, -B, -U, and -d during parsing. It checks effective mismatch penalties and gap-open-plus-extension sums after scoring setup and after --meth defaults.
Scoring bounds and regression coverage docs/src/cli/mem.md, docs/src/whats-different/equivalence.md, test/regression/arg_range_validation.sh, test/regression/meth_collapsed_scoring.sh, test/regression/README.md
Documentation describes scoring bounds and prior failure modes. Regression tests cover invalid values, accepted boundaries, presets, and --meth settings.
The CLI rejects -A below 1. Unit tests check the envelope predicate for positive, zero, and negative scores, and verify that its result does not depend on skip_contained_ext. The regression test checks that -A -1 and -A 0 are rejected.
fg-labs/bwa-mem3#617: Changes SIMD ksw_global2 scoring and preserves the -128 score case under -B 128, which this change accepts as a boundary.
fg-labs/bwa-mem3#616: Changes SIMD banded-SW score handling and tests the -128 score case under -B 128, which this change accepts as a boundary.
Merge Risk: Minimal · up to 78102
The added tests carry the required suite tags, with no remaining merge-blocking risk identified.
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Equivalence Contract Updated
The PR changes scoring validation in src/fastmap.cpp and documents the resulting divergence in docs/src/whats-different/equivalence.md, including the #634 entry and the affected scoring cases. N…
Kernel Change Validation Reported
The pull request does not modify src/bandedSWA.cpp, src/kswv.cpp, src/ksw.cpp, src/neon_utils.h, or src/simd_compat.h. The kernel-change reporting requirement does not apply.
Simd Tier Coverage
The diff does not modify SIMD kernels, tier dispatch, SIMD_WIDTH-dependent buffers, or intrinsic code. The only source change is scoring-option validation and help text in src/fastmap.cpp; other chang…
Full details: Equivalence Contract Updated
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The PR changes scoring validation in src/fastmap.cpp and documents the resulting divergence in docs/src/whats-different/equivalence.md, including the #634 entry and the affected scoring cases. No listed SAM/BAM emission implementation file changed.
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The diff does not modify SIMD kernels, tier dispatch, SIMD_WIDTH-dependent buffers, or intrinsic code. The only source change is scoring-option validation and help text in src/fastmap.cpp; other changes are documentation and tests. Therefore the SIMD-tier coverage condition is not applicable.
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Review comments at @test/unit/test_skip_contained_envelope.cpp:
- Line 34: Add the `doctest::test_suite("unit/extension")` tag to all three
`TEST_CASE` declarations for the contained-seed skip envelope tests so they run
when the `unit/extension` suite is selected.
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-A, -B, -d and -U were parsed with atoi and never range-checked, so values
a user can pass abort, wrap, overflow or give tier-dependent output:
- The match score and the negated mismatch penalty are stored in int8_t
(bwa_fill_scmat, the kswv constructor, the --meth matrices). -A 128
wraps to -128, and -A 256 zeroes kswv's maximum substitution score,
which the score2 window divides by (SIGFPE at AVX-512BW). -A 127 alone
scales the default -B to 508, which wraps to a positive mismatch score.
- A match score of 0 or less leaves nothing to align: -A 0 makes the same
kswv divide trap on x86, and with negative scores the pairing score
(mem_pair's packed key) and raw_mapq overflow, resolving differently
per ISA. A negative -B scores a mismatch above zero, which breaks the
8-bit kernels' admission tests (they take -A as the largest per-base
score) and the mapping-quality identity term (it divides by a + b).
On 200k WGS pairs, -A -1, -B -4 and -B -127 each gave different records
across AVX2, AVX-512BW and NEON, with UBSan overflows at those sites.
- -d -1 aborts on the 8-bit banded extension's zdrop >= 0 assertion.
- An -O + -E sum of 2^29 or more overflows int in ksw_global2, whose
out-of-band cells sit at -2^30.
- -U near INT_MIN overflows the paired-end `score - pen_unpaired`.
-A is now parsed as an integer in 1..127, -B as a complete int, and -d
and -U as non-negative ints. Because -A is positive, update_a's scaling
keeps every sign and stays inside int. check_effective_scoring() then
checks the effective values after -A scaling and the -x presets, and
again after the --meth defaults: the mismatch penalty must be in 0..128
and each gap open + extension sum at most 2^29 - 1, each refusal
reporting the effective value and the options behind it.
-A -1 and -A 0 were the contained-seed skip's proof-envelope legs in
compat_contained_skip_identity.sh; they are now parse refusals there,
and the envelope predicate is unit-tested instead. Every newly refused
scoring crashed, wrapped, overflowed or gave tier-dependent output
before, except a negative -U.
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Summary
-A,-B,-dand-Uwere parsed withatoiand never range-checked, so values a user can pass abort, wrap, overflow or give different output per SIMD tier:int8_t(bwa_fill_scmat, thekswvconstructor, the--methmatrices).-A 128wraps to -128, and-A 256(or any scoring that wraps the maximum substitution score to 0) makes the mate-rescue kernel's score2 window divide by zero.-A 127alone scales the default-Bto 508, which wraps to a positive mismatch score.-Aas the largest per-base score) and the mapping-quality identity term (it divides bya + b). Measured on 200k WGS pairs on AMD Zen 4 (AVX2 and AVX-512BW, forced) and AWS Graviton 4 (NEON), clang 19.1.7, with the penalties pinned:-A 0: SIGFPE on both x86 tiers (the score2 divide); NEON runs, with UBSan reporting the division by zero.-A -1: AVX2 and AVX-512BW agree, NEON gives a different record set; UBSan reports a float-to-int overflow in the pairing score (mem_pairreads a negative score back from its unsigned key).-B -4and-B -127: all three tiers give different record sets; UBSan reports an overflow inraw_mapq.-d -1aborts on the 8-bit banded extension'szdrop >= 0assertion (live in release builds).-O+-Esum of 2^29 or more overflowsintinksw_global2, whose out-of-band cells sit at -2^30 and loseo + etwice more;-O 536870912overflows and still exits 0.-UnearINT_MINoverflows the paired-endscore - pen_unpaired.Now:
-Amust be an integer in 1..127,-Ba completeint, and-dand-Unon-negativeints. With-Apositive,update_a's scaling keeps every sign and stays insideint(only built-in defaults are scaled; the largest product is 127 × 100).check_effective_scoring()checks the effective values after-Ascaling and the-xpresets, and again after the--methdefaults: mismatch penalty in 0..128 and each gap open + extension sum ≤ 2^29 - 1. Each refusal reports the effective value and the options behind it, like the existing--methmismatch-penalty check. Witha ≥ 1andb ≥ 0, the mapping-quality divisora + bis at least 1. The sign checks on the gap penalties, z-drop and unpaired penalty are gone from the effective check: their parse checks plus a positive-Aalready guarantee them.Decisions:
-A 0and a negative-Aare refused even with every penalty given. They used to be the contained-seed skip's proof-envelope legs incompat_contained_skip_identity.sh; those legs now check the refusal, and the envelope predicate (mem_skip_contained_ext_sound,a >= 0) gets a unit test. The driver's guard and its notice stay, unreachable from the command line.-Bis refused on every path.-B 0stays accepted off--meth(it only affects placement), and--methkeeps refusing it.-Uis refused; it ran before (a bonus for leaving a pair unpaired, which the pairing code does not expect).-A 127alone is refused because it scales the default-Bto 508;-A 127 -B 4runs. The largest-Athat runs without-Bis 32.The messages:
Output change
None for any scoring that is accepted. Every newly refused scoring crashed, wrapped, overflowed or gave tier-dependent output before, except a negative
-U. Documented under "Degenerate numeric inputs" inwhats-different/equivalence.md, with the ranges added to thememoption reference and the usage text.Out of scope: the kswv kernel's own guard against a zero maximum substitution score and its dead-group score2 write (#633), and
-T/-L, which are not range-checked here.Test plan
arg_range_validation.sh: refusals for-A 128/256/20000000/2x/0/-1/-128,-A 0and-A -1with every penalty pinned,-B 129/-1/-4/-127/4x,-A 4 -B -4,-A 33and-A 127(effective-B),-d -1/5x,-U -1/-2147483647/5x, and-O/-Esums one past the bound for each gap type; acceptance checks (each run must reach index loading with no scoring refusal) for defaults,-A 1/2/32,-A 127 -B 4,-B 0/128,-d 0 -U 0,-O 536870910, the three-xpresets,--meth,--meth -A 2and--meth-scoring genomic -A 32compat_contained_skip_identity.sh: the-A -1and-A 0envelope legs now assert the parse refusal;test/unit/test_skip_contained_envelope.cpppins the predicate's boundarymeth_collapsed_scoring.sh:--meth -B 0is refused by the--methguard,--meth -B -1by the scoring check; the-A 0route is gone-fsyntax-onlyofsrc/fastmap.cppand the new unit test; shellcheck and shfmt clean; README contract, regression coverage, shell and NDEBUG lints pass locallySummary by CodeRabbit
-Aoption accepts only values from 1 to 127; negative values and zero are rejected.-Ais below 1.