Add some extension to the dorado plugin, causing it to set the alignments returned from dorado onto the basecalling result.
Not bothering with Guppy, as it's old.
Also sets reconnect_timeout and server_file_load_timeout to 10 on the PyBasecallClient by default meaning we timeout after 10 seconds rather than waiting for 5 minutes 5 times.
Add some code to the _mappy to create a PAF record from a list of fields, which is useful for converting the alignment data off the basecall record to a PAF.
Adds some documentation about using it to TOML.md.
Added the get_item function to deal with structured numpy arrays, which nested_get couldn't do ( I think ).
Notable
This method means it is absolutely possible to use both dorado to align as well as mappy, if mapper_settings isn't set to no_op.
Any thoughts?
Add some extension to the dorado plugin, causing it to set the alignments returned from dorado onto the basecalling result.
Not bothering with Guppy, as it's old.
Also sets reconnect_timeout and server_file_load_timeout to 10 on the
PyBasecallClientby default meaning we timeout after 10 seconds rather than waiting for 5 minutes 5 times.Add some code to the
_mappyto create a PAF record from a list of fields, which is useful for converting the alignment data off the basecall record to a PAF.Adds some documentation about using it to TOML.md.
Added the
get_itemfunction to deal with structured numpy arrays, whichnested_getcouldn't do ( I think ).Notable
This method means it is absolutely possible to use both dorado to align as well as mappy, if mapper_settings isn't set to
no_op. Any thoughts?