compress

compress compresses a placefile’s pqueries.

usage: compress [options] placefile

Options

--point-mass	Treat every pquery as a point mass concentrated on the highest-weight placement.
--pp	Use posterior probability for the weight.
-o	Specify the filename to write to.
--out-dir	Specify the directory to write files to.
--prefix	Specify a string to be prepended to filenames.
--cutoff	The cutoff parameter for mass compression
--discard-below
	In island clustering, ignore pquery locations with a mass less than the specified value.
--mcl	Use MCL clustering instead of island clustering.
--inflation	If specified, pass this as the inflation value to MCL.

Details

A cutoff c is specified via a command line flag. The compress command merges pairs of pqueries that have KR distance between them less than c.

To compress the pqueries:

• divide the pqueries into sets via islands or mcl
• for each pquery set, calculate all of the pairwise distances between the pqueries for that island and put them in a matrix
• build a graph such that the nodes are pqueries, and there is an edge between them if their distance is less than c
• merge pqueries according to this graph as described below.

Each original pquery (=node) will get merged into one of the the selected pqueries. This will happen as follows. Maintain a set of unmerged pqueries, and a set of pairs (w, d(w)), where w is a selected pquery and d(w) is the degree of w in the graph.

• find the (w, d(w)) pair with the greatest d(w) and remove it from the set
• find all of the unmerged pqueries that are adjacent to w in the graph, and merge their mass into w. Remove w and all of the adjacent pqueries from the unmerged pquery set.
• repeat!

Stop when the unmerged pquery set is empty.