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Fix out-of-bounds read in createAsciiSubMat (segfault in rescorediagonal ungapped scoring) #1132

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Merged
martin-steinegger merged 1 commit into from
Sep 13, 2026
+8 −2
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Fix out-of-bounds read in createAsciiSubMat (segfault in rescorediagonal ungapped scoring) #1132

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10 changes: 8 additions & 2 deletions src/commons/SubstitutionMatrix.h
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
// If a probabilities file is given, it calculates a biased matrix (produces shorter = more precise alignments).
//

#include <climits>
#include <cstddef>
#include "BaseMatrix.h"
#include "ProfileStates.h"
Expand Down Expand Up @@ -51,10 +52,15 @@ class SubstitutionMatrix : public BaseMatrix {
{}
};

// build matrix from ~ (=0) to ~(=122)
// Build a table covering every byte value that aa2num maps (0..UCHAR_MAX-1), not just
// the printable-ASCII range up to 'z'. DistanceCalculator.h's ungapped scoring functions
// index this table directly with raw, untranslated byte values (not routed through
// aa2num first), so any byte the table doesn't cover reads past the end of `matrix` and
// crashes on dereference. aa2num's own mapping (see SubstitutionMatrix::setupLetterMapping)
// already sends every unmapped byte to the 'X' index, so widening this table is safe.
static FastMatrix createAsciiSubMat(BaseMatrix & submat){
const size_t asciiStart = 0;
const size_t asciiEnd = 'z'+1;
const size_t asciiEnd = UCHAR_MAX;
const size_t range = asciiEnd-asciiStart;
char ** matrix = new char *[range];
char * matrixData = new char[range*range];
Expand Down