Pranav Ballaney pushed to branch master at Debian Med / kallisto
Commits: 9af9aec0 by Pranav Ballaney at 2020-05-16T04:39:07+05:30 Patch to avoid segfault - - - - - 2 changed files: - + debian/patches/Check_busOptions.seq_length_before_accessing.patch - debian/patches/series Changes: ===================================== debian/patches/Check_busOptions.seq_length_before_accessing.patch ===================================== @@ -0,0 +1,32 @@ +Description: Check busOptions.seq.empty() before trying to access it, + to avoid a segfault. More details can be found at the upstream bug. +Author: Pranav Ballaney <[email protected]> +Bug: https://github.com/pachterlab/kallisto/issues/254 +Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960368#15 +Last-Update: 2020-05-16 +--- +This patch header follows DEP-3: http://dep.debian.net/deps/dep3/ +--- a/src/ProcessReads.cpp ++++ b/src/ProcessReads.cpp +@@ -1408,6 +1408,12 @@ void BUSProcessor::processBuffer() { + std::vector<int> l(jmax,0); + + bool singleSeq = busopt.seq.size() ==1 ; ++ ++ if (mp.opt.busOptions.seq.empty()) { ++ std::cerr << "No seq technology specified.\n"; ++ std::cerr << "If you believe this is a bug, please report using reportbug."; ++ std::cerr.flush(); ++ } + const BUSOptionSubstr seqopt = busopt.seq.front(); + + +@@ -2145,7 +2151,7 @@ void AlnProcessor::processBufferGenome() + rlen2 = seqs[si2].second; + } + +- if (mp.opt.busOptions.seq.front().fileno == 1) { ++ if (!mp.opt.busOptions.seq.empty() && mp.opt.busOptions.seq.front().fileno == 1) { + std::swap(si1,si2); + std::swap(rlen1,rlen2); + } ===================================== debian/patches/series ===================================== @@ -1,3 +1,4 @@ use_debian_packaged_htslib.patch spelling htslib1.3 +Check_busOptions.seq_length_before_accessing.patch View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/commit/9af9aec0b4000395bdd9bdfa0e97aa9551bce9a3 -- View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/commit/9af9aec0b4000395bdd9bdfa0e97aa9551bce9a3 You're receiving this email because of your account on salsa.debian.org.
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