Let Scanpy read from Cell Ranger 3.0 outputs

[qianggong11]

Hi @falexwolf,

10X is releasing a new version of CellRanger that is changing the output format. This pull request makes Scanpy forward compatible with the new version. In particular, the following changes are made:

Updated read_10x_h5:

• Renamed the original read_10x_h5 as _read_legacy_10x_h5;
• Added _read_v3_10x_h5 to read the new Cell Ranger output format;
• The new read_10x_h5 determines the version of HDF5 input by the presence of the matrix key, and wraps the above two functions. In addition, it takes a gex_only argument which filters out feature barcoding counts from the outcome object when it is True (default). Otherwise, the full matrix will be retained.
• For CR-v3, feature_types and genome were added into the outcome object as new attributes.

Updated read_10x_mtx:

• Renamed the original read_10x_mtx as _read_legacy_10x_mtx;
• Added _read_v3_10x_mtx to read the new Cell Ranger output format;
• The new read_10x_mtx determines the version of matrix input by the presence of the genes.tsv file under the input directory, and wraps the above two functions. In addition, it takes a gex_only argument which filters out feature barcoding counts from the outcome object when it is True (default). Otherwise, the full matrix will be retained.
• For CR-v3, feature_types was added into the outcome object as a new attribute.

Added small test datasets and code for the revised functions to verify the expected behavior.

Note for the genome argument:

• There is a genome argument in Scanpy's read_10x_h5 function but not in read_10x_mtx as the genome was already specified by the path of input directory. The outcome object of the two functions should be the same which always take one genome at a time.
• In this PR, when there are multiple genomes (e.g. Barnyard), read_10x_mtx always read them all, whereas read_10x_h5 always need to specify one of them (mm10 by default). However, when gex_only == False, the genome argument will be ignored and the whole matrix will be read.

[falexwolf]

Thank you very much! That looks good!

Alex