[med-svn] [Git][med-team/kallisto][master] 2 commits: Patch to avoid segfault - exit with an error

[Pranav Ballaney]

Pranav Ballaney pushed to branch master at Debian Med / kallisto


Commits:
801c272b by Pranav Ballaney at 2020-05-16T04:47:02+05:30
Patch to avoid segfault - exit with an error

- - - - -
547fd1b6 by Pranav Ballaney at 2020-05-16T04:47:43+05:30
Update changelog

- - - - -


2 changed files:

- debian/changelog
- debian/patches/Check_busOptions.seq_length_before_accessing.patch


Changes:

=====================================
debian/changelog
=====================================
@@ -1,3 +1,9 @@
+kallisto (0.46.2+dfsg-2) UNRELEASED; urgency=medium
+
+  * Patch to avoid segfault (Closes: #960368)
+
+ -- Pranav Ballaney <ballaneypranav at gmail.com>  Sat, 16 May 2020 04:47:12 +0530
+
 kallisto (0.46.2+dfsg-1) unstable; urgency=medium
 
   * Team upload.


=====================================
debian/patches/Check_busOptions.seq_length_before_accessing.patch
=====================================
@@ -2,13 +2,13 @@ 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
+Bug-Debian: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=960368
 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() {
+@@ -1408,6 +1408,13 @@ void BUSProcessor::processBuffer() {
    std::vector<int> l(jmax,0);
  
    bool singleSeq = busopt.seq.size() ==1 ;
@@ -17,11 +17,12 @@ This patch header follows DEP-3: http://dep.debian.net/deps/dep3/
 +    std::cerr << "No seq technology specified.\n";
 +    std::cerr << "If you believe this is a bug, please report using reportbug.";
 +    std::cerr.flush();
++    exit(1);
 +  }
    const BUSOptionSubstr seqopt = busopt.seq.front();
  
  
-@@ -2145,7 +2151,7 @@ void AlnProcessor::processBufferGenome()
+@@ -2145,7 +2152,7 @@ void AlnProcessor::processBufferGenome()
        rlen2 = seqs[si2].second;
      }
      



View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/compare/9af9aec0b4000395bdd9bdfa0e97aa9551bce9a3...547fd1b6a0fade81dea21e8f1093b1ef2c6961c6

-- 
View it on GitLab: https://salsa.debian.org/med-team/kallisto/-/compare/9af9aec0b4000395bdd9bdfa0e97aa9551bce9a3...547fd1b6a0fade81dea21e8f1093b1ef2c6961c6
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