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Structural Variation Graph (sv graph) Thoughts

Posted in programming, research by ryanlayer on January 5, 2010

The data structure consists of:

– a set of chromosomes

– each chromosome is represented by a name, and an ordered (doublely linked) list of nodes

– each node represents one tag of a pair

– each node has a double sided link to the next node in chromosome order (the node with the next largest offset), and a list of nodes in which the node is part of a pair.  The links to the pairs are one-way.

The chromosome name is not part of the node struct.  Each node does have a pointer back to it’s chromosome structure, and that chromosome struct contains the name.  This prevents a potentially long chromosome name from being stored a ton of time (in each node).  When we are reading the nodes from a file, we must pass in a char pointer so that the name of the chromosome can be set.  We will use this char pointer to put the node into the proper chromosome structure.

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