BedTool.filter silently ignoring exceptions

[pkaleta]

Here's an example that demonstrates the issue:

In [76]: def foo(x):
    raise ValueError('foo')
   ....:

In [77]: list(bed.filter(foo))
Out[77]: []

In [78]: [x for x in bed if foo(x)]
---------------------------------------------------------------------------
ValueError                                Traceback (most recent call last)
<ipython-input-78-3c60a1efa4e0> in <module>()
----> 1 [x for x in bed if foo(x)]

<ipython-input-76-45cfbd08b10a> in foo(x)
      1 def foo(x):
----> 2     raise ValueError('foo')
      3

ValueError: foo

As you can see, when using filter the exception is ignored somewhere along the way. I believe that the reason is that you're catching ValueError here: https://github.com/daler/pybedtools/blob/master/pybedtools/cbedtools.pyx#L760

[daler]

Thanks for reporting. I agree, that except (StopIteration, ValueError): is the likely culprit. That's part of a fix for a Cython idiosyncrasy (that was really tricky to pin down at the time) and I hesitate to change it without extensive testing.

Maybe as an alternative, BedTool.filter could wrap the incoming function, and the wrapper could replace any exceptions with FilterFunctionError that wouldn't get trapped by IntervalIterator.__next__?

[daler]

Addressed in #264