Jeff S Jasper

VCF files should be block-gzipped and not gzipped

4

Excellent package! I have prototyped a few solutions to use this to apply ML classification of called variants and do filtering. This is more of a feature request. Just wanted...

Salmon quant

2

As is, starseqr always requires fatqs even if a STAR alignment is provided. If we modify the salmon call to do alignment mode in this scenario we can bypass the...

The latest networkx2.1rc1 version renames several functions. Specifically: ``` adj_mat = nx.to_pandas_dataframe(node_graph) AttributeError: 'module' object has no attribute 'to_pandas_dataframe' ``` The function is now called `to_pandas_adjacency` per: https://github.com/networkx/networkx/pull/2811 Either specify...

Potential future issue

1

/pandas/core/groupby.py:3961: FutureWarning: using a dict with renaming is deprecated and will be removed in a future version return super(DataFrameGroupBy, self).aggregate(arg, *args, **kwargs)

Feature request: split by chromosome

2

Biobambam2 is an incredibly useful package and it seems like I am constantly discovering new features and applications. It would be helpful if the readme had a short description or...