nvictus/pybbi

segfault with fetch_intervals

nvictus opened this issue · 1 comments

Using the following bigbed file: https://www.encodeproject.org/files/ENCFF662CHC/

In [1]: import bbi

In [2]: list(bbi.fetch_intervals('./ENCFF662CHC.bigBed', 'chr1', 0, 100))
*** Error in `/home/nezar/miniconda3/bin/python': free(): invalid pointer: 0x0000000003127e40 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x777e5)[0x7f014801c7e5]
/lib/x86_64-linux-gnu/libc.so.6(+0x7fe0a)[0x7f0148024e0a]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x4c)[0x7f014802898c]
/home/nezar/local/devel/bbifile/pybbi/bbi/cbbi.cpython-35m-x86_64-linux-gnu.so(+0x35206)[0x7f0140d8a206]
/home/nezar/local/devel/bbifile/pybbi/bbi/cbbi.cpython-35m-x86_64-linux-gnu.so(+0x288a9)[0x7f0140d7d8a9]
/home/nezar/miniconda3/bin/../lib/libpython3.5m.so.1.0(+0xa06ee)[0x7f0148f436ee]
/home/nezar/miniconda3/bin/../lib/libpython3.5m.so.1.0(+0xa0b48)[0x7f0148f43b48]
/home/nezar/miniconda3/bin/../lib/libpython3.5m.so.1.0(+0xcedaf)[0x7f0148f71daf]
/home/nezar/miniconda3/bin/../lib/libpython3.5m.so.1.0(PyObject_Call+0x56)[0x7f0148f0a236]
/home/nezar/miniconda3/bin/../lib/libpython3.5m.so.1.0(PyEval_EvalFrameEx+0x66f4)[0x7f0148fe4314]
/home/nezar/miniconda3/bin/../lib/libpython3.5m.so.1.0(+0x144b49)[0x7f0148fe7b49]
/home/nezar/miniconda3/bin/../lib/libpython3.5m.so.1.0(PyEval_EvalCodeEx+0x48)[0x7f0148fe7cd8]
...

A spurious free() seemed to be the problem.