Topological Sorts
-b, –breadth-first
Use a (chunked) breadth first topological sort.
-B, –breadth-first-chunk=N
Chunk size for breadth first topological sort. Specify how many
nucleotides to grap at once in each BFS phase.
-z, –depth-first
Use a (chunked) depth first topological sort.
-Z, –depth-first-chunk=N
Chunk size for the depth first topological sort. Specify how many
nucleotides to grap at once in each DFS phace.
-w, –two-way
Use a two-way topological algorithm for sorting. It is a maximum of
head-first and tail-first topological sort.
-n, –no-seeds
Don’t use heads or tails to seed topological sort.
-c, –cycle-breaking
Use a cycle breaking sort.
Path Guided 1D Linear SGD Sort
-Y, –path-sgd
Apply path guided 1D linear SGD algorithm to organize the graph.
-X, –path-index=FILE
Load the path index from this FILE.
-f, –path-sgd-use-paths=FILE
Specify a line separated list of paths to sample from for the on the
fly term generation process in the path guided linear 1D SGD. The
default value are all paths.
-G, –path-sgd-min-term-updates-paths=N
The minimum number of terms to be updated before a new path guided
linear 1D SGD iteration with adjusted learning rate eta starts,
expressed as a multiple of total path steps. The default value is
1.0. Can be overwritten by -U, -path-sgd-min-term-updates-nodes=N.
-U, –path-sgd-min-term-updates-nodes=N
The minimum number of terms to be updated before a new path guided
linear 1D SGD iteration with adjusted learning rate eta starts,
expressed as a multiple of the number of nodes. Per default, the
argument is not set. The default of -G,
path-sgd-min-term-updates-paths=N is used).
-j, –path-sgd-delta=N
The threshold of maximum displacement approximately in bp at which to
stop path guided linear 1D SGD. Default values is 0.0.
-g, –path-sgd-eps=N
The final learning rate for path guided linear 1D SGD model. The
default value is 0.01.
-v, –path-sgd-eta-max=N
The first and maximum learning rate for path guided linear 1D SGD
model. The default value is squared steps of longest path in graph.
-a, –path-sgd-zipf-theta=N
The theta value for the Zipfian distribution which is used as the
sampling method for the second node of one term in the path guided
linear 1D SGD model. The default value is 0.99.
-x, –path-sgd-iter-max=N
The maximum number of iterations for path guided linear 1D SGD model.
The default value is 30.
-F, –iteration-max-learning-rate=N
The iteration where the learning rate is max for path guided linear 1D
SGD model. The default value is 0.
-k, –path-sgd-zipf-space=N
The maximum space size of the Zipfian distribution which is used as
the sampling method for the second node of one term in the path guided
linear 1D SGD model. The default value is the longest path length.
-I, –path-sgd-zipf-space-max=N
The maximum space size of the Zipfian distribution beyond which
quantization occurs. Default value is 100.
-l, –path-sgd-zipf-space-quantization-step=N
Quantization step size when the maximum space size of the Zipfian
distribution is exceeded. Default value is 100.
-y, –path-sgd-zipf-max-num-distributions=N
Approximate maximum number of Zipfian distributions to calculate. The
default value is 100.
-q, –path-sgd-seed=N
Set the seed for the deterministic 1-threaded path guided linear 1D
SGD model. The default value is pangenomic!.
-u, –path-sgd-snapshot=STRING
Set the prefix to which each snapshot graph of a path guided 1D SGD
iteration should be written to. This is turned off per default. This
argument only works when -Y, –path-sgd was specified. Not applicable
in a pipeline of sorts.
Path Sorting Options
-L, –paths-min
Sort paths by their lowest contained node identifier.
-M, –paths-max
Sort paths by their highest contained node identifier.
-A, –paths-avg
Sort paths by their average contained node identifier.
-R, –paths-avg-rev
Sort paths in reverse by their average contained node identifier.
-D, –path-delim=path-delim
Sort paths in bins by their prefix up to this delimiter.