good catch


On Mon, Jan 6, 2014 at 10:54 AM, Jai Ram Rideout
<notifications@github.com>wrote:

> In biom/table.py:
>
> > +        # advantage here is to limit the number of datasets in h5grp to O(N)
> > +        # where N is the number of samples. In addition, it explicitly keeps
> > +        # the values and observation indices in index order.
> > +        for s_idx, (v, i, m) in enumerate(self.iterSamples(conv_to_np=False)):
> > +            ### would benefit from iterSamples doing direct slices here
> > +            coo = v._matrix.tocoo()
> > +
> > +            # ./data/<sample_name>
> > +            samp_grp = data_grp.create_group(i)
> > +            samp_grp.attrs['sample_id_index'] = int32(s_idx)
> > +
> > +            # A sample may have an external link to tie against the observation
> > +            # map which would allow back tracking to determine the specific
> > +            # sequences associated with a (sample, observation).
> > +            if self.SampleExtLink is not None:
> > +                f, p = self.SampleExtLink[s_idx] # f -> file, p -> path
>
> When the HDF5 file is parsed, the order of external links isn't guaranteed
> (iterating over a dictionary-like structure), nor is it guaranteed that
> each sample will have an external link.
>
> —
> Reply to this email directly or view it on GitHub<https://github.com/biom-format/biom-format/pull/268/files#r8671530>
> .
>