GFA
Types
PanGraph.Graphs.GFA.Path
— Typestruct Path
name :: String
segments :: Array{Node,1}
circular :: Bool
end
Store a GFA path, i.e. a sequence of segments that represents an observed genome.
PanGraph.Graphs.GFA.Segment
— Typestruct Segment
name :: String
sequence :: Array{UInt8}
depth :: Int
end
Store a GFA segment, i.e. an edge of an alignment graph that holds a contiguous sequence Depth is the number of genomes, including duplications, that contain the sequence.
Functions
PanGraph.Graphs.marshal_gfa
— Methodmarshal_gfa(io::IO, G::Graph; opt=nothing)
Output pangraph G
to IO stream io
. opt
can include two functions, to be accessed in fields connect
and output
. connect
is a function that takes a node and returns true or false if it should be connected in the GFA output. output
is an equivalent function signature, but controls whether the node is output at all.