add check_integrity utility that can be called at key places, including Cooler instantiation
(if indexes are missing, cooler cli currently fails with uninformative errors, as below)
cooler coarsen --out test.cool
Traceback (most recent call last):
File "/home/gfudenberg/anaconda3/bin/cooler", line 11, in
load_entry_point('cooler', 'console_scripts', 'cooler')()
File "/home/gfudenberg/anaconda3/lib/python3.6/site-packages/click/core.py", line 722, in call
return self.main(*args, **kwargs)
File "/home/gfudenberg/anaconda3/lib/python3.6/site-packages/click/core.py", line 697, in main
rv = self.invoke(ctx)
File "/home/gfudenberg/anaconda3/lib/python3.6/site-packages/click/core.py", line 1066, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/gfudenberg/anaconda3/lib/python3.6/site-packages/click/core.py", line 895, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/gfudenberg/anaconda3/lib/python3.6/site-packages/click/core.py", line 535, in invoke
return callback(*args, **kwargs)
File "/home/gfudenberg/anaconda3/lib/python3.6/site-packages/cooler/cli/aggregate.py", line 286, in coarsen
lock=lock if same_file else None)
File "/home/gfudenberg/anaconda3/lib/python3.6/site-packages/cooler/cli/aggregate.py", line 45, in aggregate
map=pool.map if nproc > 1 else map)
File "/home/gfudenberg/anaconda3/lib/python3.6/site-packages/cooler/_binning.py", line 504, in init
self.old_chrom_offset = clr._load_dset('indexes/chrom_offset')
File "/home/gfudenberg/anaconda3/lib/python3.6/site-packages/cooler/api.py", line 87, in _load_dset
return grp[path][:]
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/h5py_1482475225177/work/h5py/_objects.c:2856)
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/h5py_1482475225177/work/h5py/_objects.c:2814)
File "/home/gfudenberg/anaconda3/lib/python3.6/site-packages/h5py/_hl/group.py", line 166, in getitem
oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/h5py_1482475225177/work/h5py/_objects.c:2856)
File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper (/home/ilan/minonda/conda-bld/h5py_1482475225177/work/h5py/_objects.c:2814)
File "h5py/h5o.pyx", line 190, in h5py.h5o.open (/home/ilan/minonda/conda-bld/h5py_1482475225177/work/h5py/h5o.c:3742)
KeyError: 'Unable to open object (Component not found)'
open2c
