[Debian-med-packaging] Bug#853859: bwa: Segmentation fault with specific data set

[Andreas Tille]

Package: bwa
Severity: normal

Hi,

I've uploaded an archive containing a data set[1] that leads to a
segfault when doing

  bwa bwasw -t 20 00-optrApE349.fas 2708-UW15005_S1_L001_R1_001.fastq.gz 2708-UW15005_S1_L001_R2_001.fastq.gz -f test.sam

The compressed tar archive contains the data set, a script named
run_bwa_Segmentation_fault you can simply run to reproduce the issue and
the output of the run in the file bwa.out.  I have tested the problem
with four versions of bwa (0.7.10, 0.7.14 and 0.7.15) all with the same
result.

The issue has been forwarded upstream[2] and this bug is here to inform
other Debian users about the issue.  (For sure any volunteer can come up
with a patch.)

Kind regards

      Andreas.

[1] https://people.debian.org/~tille/tmp/bwa/bwa_segmentation_fault.tar.gz
[2] https://github.com/lh3/bwa/issues/108

-- System Information:
Debian Release: 8.7
  APT prefers stable-updates
  APT policy: (500, 'stable-updates'), (500, 'stable')
Architecture: amd64 (x86_64)

Kernel: Linux 3.16.0-4-amd64 (SMP w/1 CPU core)
Locale: LANG=de_DE.UTF-8, LC_CTYPE=de_DE.UTF-8 (charmap=UTF-8)
Shell: /bin/sh linked to /bin/dash
Init: systemd (via /run/systemd/system)

Versions of packages bwa depends on:
ii  libc6   2.19-18+deb8u7
ii  zlib1g  1:1.2.8.dfsg-2+b1

bwa recommends no packages.

Versions of packages bwa suggests:
pn  samtools  <none>