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Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.
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segfaults when m_breakDancerMask is accessed outside itself #5

Open joelmartin opened 10 years ago

joelmartin commented 10 years ago

when -Q reporting breakdancer events is turned on pindel segfaults in BDData::isBreakDancerEvent in bddata.cpp, also reported by 'aguitarfreak' on biostarts. for both of us it's happening at m_breakDancerMask[ rawLeftPosition - m_currentWindow.getStart() ](or rawRightPosition - m_currentWindow.getStart%28%29) and rawLeft/RightPosition is outside m_breakDancerMask[ m_currentWindow.getStart ] array size.

isBreakDancerEvent: initialized : rawLeft 17734564 window.getstart: 15097000 rawRight: 17734644 isBreakDancerEvent: initialized : rawLeft 17888942 window.getstart: 15097000 rawRight: 17889750 isBreakDancerEvent: initialized : rawLeft 8017842 window.getstart: 15097000 rawRight: 18783914 [segfaults here of course] for the biostars person it was rawLeft 4239970296 - window.getstart 55097000

wyleung commented 8 years ago

Is this still a valid bug? I have not checked this ever since. ref biostars: https://www.biostars.org/p/107437/