[med-svn] [Git][med-team/kallisto][master] Patch to avoid segfault

[Pranav Ballaney]

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 <ballaneypranav at gmail.com>
+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
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