On Wed, 20 Nov 2024 21:48:23 +0100 =?utf-8?Q?=C3=89tienne?= Mollier
<emoll...@debian.org> wrote:
Control: retitle -1 blasr: autopkgtest failure: core dump
Control: tags -1 + help
...
#7 RemoveOverlappingAnchors<std::vector<ChainedMatchPos,
std::allocator<ChainedMatchPos> > > (matchList=std::vector of length 34, capacity 64
= {...})
at
/usr/include/pbseq/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp:144
#8 0x00005555555cd01f in MapRead<SMRTSequence, FASTASequence, SuffixArray<unsigned char, std::vector<int, std::allocator<int> >, DefaultCompareStrings<unsigned char>, DNATuple>, TupleCountTable<FASTASequence, DNATuple> > (read=...,
Thanks for debugging this. The error to me appears to be here:
https://salsa.debian.org/med-team/pbseqlib/-/blob/master/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp?ref_type=heads#L140
and consequently at
https://salsa.debian.org/med-team/pbseqlib/-/blob/master/alignment/algorithms/anchoring/FindMaxIntervalImpl.hpp?ref_type=heads#L144
It is then trying to access matchList[m] and m is matchList.size() in
the first iteration which is undefined behavior.
It should start from matchList.size() - 1. I've pushed a fix -- do
blasr autopkgtest pass now?
If it looks fine, could you sponsor me an upload?
Thanks
Nilesh
