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Issue #7 resolved

testFragmentHiC.py generates error

Anonymous created an issue

Dear colleagues, After installation of hi-c (and all additional packages Cython-0.19.1; Python-2.7.5;biopython-1.61; h5py-2.1.3;hdf5-1.8.11;james_taylor-bx-python-83b6d153f889; joblib-master;matplotlib-1.2.1;numpy-1.7.0;pysam-0.7.4;scipy-master;mirnylib) I ran some tests and I've got an error running testFragmentHiC.py The message is the following:

Testing small/large and extreme fragment filter ----->Small/large fragments filter: keep strictly lessthan 100000,strictly more than 100 bp Traceback (most recent call last): File "testFragmentHiC.py", line 144, in <module> ), "test", "HindIII"]]) File "testFragmentHiC.py", line 68, in refine_paper TR.filterLarge() File "/ifs/storage/bionet/ada/prog/hi-c/src/hiclib/fragmentHiC.py", line 1080, in filterLarge self.fragmentFilter(self.ufragments[p]) File "/ifs/storage/bionet/ada/prog/hi-c/src/hiclib/fragmentHiC.py", line 973, in fragmentFilter m1 = arrayInArray(self.fragids1, fragments) File "/ifs/storage/bionet/ada/prog/mirny/mirnylib/numutils.py", line 533, in arrayInArray return _arrayInArray(array, filterarray) File "numutils_new.pyx", line 173, in numutils_new._arrayInArray (numutils_new.c:6778) IndexError: index 0 is out of bounds for size 0

Comments (3)

  1. mimakaev

    Fixed now. Please update the mirnylib library, and then reinstall it by running install_linux.py.

    The bug was caused by a change in behaviour of nowraparound decorator in cython.

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