Pierre Gruet pushed to branch master at Debian Med / sumaclust
Commits: b68b92e6 by Pierre Gruet at 2020-04-08T21:49:04+02:00 Reading ACGT-only sequences safely Better handling of line changes - - - - - 1aa21e7d by Pierre Gruet at 2020-04-08T21:57:46+02:00 Updating changelog - - - - - 3 changed files: - debian/changelog - + debian/patches/reading_only_ACGT_sequences_safely.patch - debian/patches/series Changes: ===================================== debian/changelog ===================================== @@ -1,3 +1,10 @@ +sumaclust (1.0.35-3) UNRELEASED; urgency=medium + + * Adding a patch to read ACGT-only sequences safely, fixing regression + on amd64 (Closes: #956232) + + -- Pierre Gruet <[email protected]> Wed, 08 Apr 2020 21:49:49 +0200 + sumaclust (1.0.35-2) unstable; urgency=medium * Updating fix_build patch after new upstream version ===================================== debian/patches/reading_only_ACGT_sequences_safely.patch ===================================== @@ -0,0 +1,40 @@ +From: Pierre Gruet <[email protected]> +Date: Wed, 8 Apr 2020 11:18:01 +0200 +Subject: Reading only-ACGT sequences safely + +--- + sumalibs/libfasta/sequence.c | 10 ++++++++-- + 1 file changed, 8 insertions(+), 2 deletions(-) + +diff --git a/sumalibs/libfasta/sequence.c b/sumalibs/libfasta/sequence.c +index 2cf3d10..db999f8 100755 +--- a/sumalibs/libfasta/sequence.c ++++ b/sumalibs/libfasta/sequence.c +@@ -162,19 +162,25 @@ void seq_fillSeqOnlyATGC(char *seq, fastaSeqPtr seqElem, int seqLen) + { + char* seqTemp; + char c; +- int32_t index = 0, seqIndex = 0, len = strlen(seq); ++ int32_t index = 1, seqIndex = 0, len = strlen(seq); + char* seqAlphabets = "acgtACGT"; + int notAllATGC = 0; ++ int goOnParsing = 1; + + seqTemp = (char*) util_malloc(seqLen*sizeof(char), __FILE__, __LINE__); + +- while (index < len) ++ while (goOnParsing) + { + c = seq[index++]; + if (strchr(seqAlphabets, c) != NULL) + seqTemp[seqIndex++] = tolower(c); ++ else if (c == '\n') ++ goOnParsing = 0; //End of line character terminating the sequence has been reached. + else if (c != '\n') + notAllATGC = 1; ++ ++ if (index == len) ++ goOnParsing = 0; + } + + if (notAllATGC) ===================================== debian/patches/series ===================================== @@ -1,2 +1,3 @@ hardening.patch fix_build.patch +reading_only_ACGT_sequences_safely.patch View it on GitLab: https://salsa.debian.org/med-team/sumaclust/-/compare/954b3e6a483f5015fc15c858211fd971848b8628...1aa21e7dde4907231c67fe9e91da8d91d54316b2 -- View it on GitLab: https://salsa.debian.org/med-team/sumaclust/-/compare/954b3e6a483f5015fc15c858211fd971848b8628...1aa21e7dde4907231c67fe9e91da8d91d54316b2 You're receiving this email because of your account on salsa.debian.org.
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