[med-svn] [Git][med-team/clustalo][master] Increase field boundaries to avoid out of range access

[Andreas Tille]

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 <tille at debian.org>  Fri, 17 Apr 2020 17:06:22 +0200
 


=====================================
debian/patches/array_out_of_bounds.patch
=====================================
@@ -0,0 +1,17 @@
+From: Matthew Fernandez <matthew.fernandez at gmail.com>
+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
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