Index with numpy int64 #143

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TypeError                                 Traceback (most recent call last)
<ipython-input-30-bec833fbac57> in <module>()
      2 sample_indices = tuple(sorted(df_samples[df_samples.population == pop].index.values))
      3 for chrom in chromosomes:
----> 4     results_by_pop[pop][chrom] = targets_accumulating_variation(chrom, sample_indices)

<ipython-input-15-8f3c421e63a5> in targets_accumulating_variation(chrom, sample_indices)
     11     sample_indices = random.sample(sample_indices, len(sample_indices))
     12     for i, sidx in enumerate(sample_indices):
---> 13         is_variant |= get_is_variant(chrom, sidx)
     14         loc = base_loc & get_target_is_conserved(is_variant)
     15         n_targets = np.count_nonzero(loc)

<ipython-input-13-dd88d658f1a4> in get_is_variant(chrom, sample_idx)
      4     out = np.zeros_like(seq, dtype=bool)
      5     pos = callset_pass[chrom]['variants/POS'][:]
----> 6     g = callset_pass[chrom]['calldata/genotype'][:, sample_idx]
      7     loc = np.any(g > 0, axis=1)
      8     idx = pos[loc] - 1

/home/aliman/miniconda3/envs/biipy_20170126_py35/lib/python3.5/site-packages/zarr/core.py in __getitem__(self, item)
    446 
    447         # normalize selection
--> 448         selection = normalize_array_selection(item, self._shape)
    449 
    450         # determine output array shape

/home/aliman/miniconda3/envs/biipy_20170126_py35/lib/python3.5/site-packages/zarr/util.py in normalize_array_selection(item, shape)
    184         # determine start and stop indices for all axes
    185         selection = tuple(normalize_axis_selection(i, l)
--> 186                           for i, l in zip(item, shape))
    187 
    188         # fill out selection if not completely specified

/home/aliman/miniconda3/envs/biipy_20170126_py35/lib/python3.5/site-packages/zarr/util.py in <genexpr>(.0)
    184         # determine start and stop indices for all axes
    185         selection = tuple(normalize_axis_selection(i, l)
--> 186                           for i, l in zip(item, shape))
    187 
    188         # fill out selection if not completely specified

/home/aliman/miniconda3/envs/biipy_20170126_py35/lib/python3.5/site-packages/zarr/util.py in normalize_axis_selection(item, l)
    163 
    164     else:
--> 165         raise TypeError('expected integer or slice, found: %r' % item)
    166 
    167 

TypeError: expected integer or slice, found: 736