classification of structural variants
We need something to go through the output VCF file and classify structural variants by their type. For example, relocations can be called by finding a deletion in one region and a (mostly) identical insertion elsewhere. Mummer has a tool for this purpose (I believe it's called show-diff
) that may be adaptable here.
The question at http://stackoverflow.com/questions/10066129/is-there-a-diff-like-algorithm-that-handles-moving-block-of-lines has some information regarding appropriate algorithms if we end up needing to do some direct implementation.
As for the output of the classification, it could be represented in VCF format since the format supports descriptions of SVs, but this can cause some information to be unrepresented if a relocation is not exact or there is some other nested variation. We could also produce a report file. Both output types could be supported and made into options.