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Update readme with -graphml flag

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efischer
2022-03-01 08:24:43 -06:00
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@@ -20,8 +20,8 @@ The problem of pairing TCRA/TCRB sequences thus reduces to the "assignment probl
matching on a bipartite graph--the subset of vertex-disjoint edges whose weights sum to the maximum possible value.
This is a well-studied combinatorial optimization problem, with many known solutions.
The most efficient algorithm known to the author for maximum weight matching of a bipartite graph with strictly integral weights
is from Duan and Su (2012). For a graph with m edges, n vertices per side, and maximum integer edge weight N,
The most efficient algorithm known to the author for maximum weight matching of a bipartite graph with strictly integral
weights is from Duan and Su (2012). For a graph with m edges, n vertices per side, and maximum integer edge weight N,
their algorithm runs in **O(m sqrt(n) log(N))** time. As the graph representation of a pairSEQ experiment is
bipartite with integer weights, this algorithm is ideal for BiGpairSEQ.
@@ -203,8 +203,9 @@ Options for creating a Graph/Data file:
These files do not have a human-readable structure, and are not portable to other programs.
(For portability to other software, turn on GraphML output in the Options menu. This will produce a .graphml file
for the weighted graph, with vertex attributes sequence, type, and occupancy data.)
(For portability to other software, turn on GraphML output in the Options menu in interactive mode, or use the -graphml
command line argument. This will produce a .graphml file for the weighted graph, with
vertex attributes for sequence, type, and occupancy data.)
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