[Debian-med-packaging] Bug#753485: samtools: python-pysam FTBFS on mips/mipsel due to issues in samtools

[Aleksandar Zlicic]

Package: samtools
Version: 0.1.19-1
Tags: sid patch
Severity: important
User: debian-mips-dev-discuss at lists.alioth.debian.org
Usertags: mips-patch

'python-pysam' package FTBFS on mips/mipsel due to issues in 'samtools' package.

Build log for 'python-pysam' on mips:
https://buildd.debian.org/status/fetch.php?pkg=python-pysam&arch=mips&ver=0.7.7-1&stamp=1397894446
Build log for 'python-pysam' on mipsel:
https://buildd.debian.org/status/fetch.php?pkg=python-pysam&arch=mipsel&ver=0.7.7-1&stamp=1397887877

Output of samtools executable from samtools package is used as a reference
during tests in python-pysam (its output is compared with output from
pysam python module), but samtools has both unaligned memory access
and system endianness issues.

I have attached patches that fix this. With these patches applied to samtools,
python-pysam builds fine.

Best Regards
Aleksandar Zlicic
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