Andreas Tille pushed to branch master at Debian Med / clustalo
Commits: 2e1ffb10 by Andreas Tille at 2020-04-19T09:19:22+02:00 Increase field boundaries to avoid out of range access - - - - - 3 changed files: - debian/changelog - + debian/patches/array_out_of_bounds.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -2,6 +2,7 @@ clustalo (1.2.4-6) UNRELEASED; urgency=medium [ Matthew Fernand ] * Fix some issues with logging calls + * Increase field boundaries to avoid out of range access -- Andreas Tille <[email protected]> Fri, 17 Apr 2020 17:06:22 +0200 ===================================== debian/patches/array_out_of_bounds.patch ===================================== @@ -0,0 +1,17 @@ +From: Matthew Fernandez <[email protected]> +Date: Fri, 17 Apr 2020 16:28:23 -0700 +Bug-Debian: https://bugs.debian.org/956324 +Origin: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=956324#64 +Description: Increase field boundaries to avoid out of range access + +--- a/src/hhalign/hhdecl-C.h ++++ b/src/hhalign/hhdecl-C.h +@@ -232,7 +232,7 @@ char program_name[NAMELEN]; //name of pr + float P[21][21]; // P[a][b] = combined probability for a aligned to b + float R[21][21]; // R[a][b]=P[a][b]/p[b]=P(a|b); precalculated for pseudocounts + float Sim[21][21]; // Similarity matrix Sim[a][b]: how similar are a and b? +-float S[21][21]; // Substitution score matrix S[a][b] = log2(Pab/pa/pb) ++float S[22][22]; // Substitution score matrix S[a][b] = log2(Pab/pa/pb) + float pb[21]; // pb[a] = background amino acid probabilities for chosen substitution matrix + float qav[21]; // qav[a] = background amino acid probabilities for query HMM (needed for rate matrix rescaling) + ===================================== debian/patches/series ===================================== @@ -1 +1,2 @@ clustalo-log-format-calls.patch +array_out_of_bounds.patch View it on GitLab: https://salsa.debian.org/med-team/clustalo/-/commit/2e1ffb10ef69e2cf8e6b0f1e8da4f81ba4c75959 -- View it on GitLab: https://salsa.debian.org/med-team/clustalo/-/commit/2e1ffb10ef69e2cf8e6b0f1e8da4f81ba4c75959 You're receiving this email because of your account on salsa.debian.org.
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