Standard output

[dbolotin]

By 2.2 we should came up with some standard, easy-parseable output for alignments and clones. No more additional pre-processing of anchor points, alignments, hits, etc.. Something maximally simple, but containing complete information about target entities.

• Python / R libs with one-command parsing to make it possible for us to make minor changes if something turns up to be wrong. In this case changes will cost users a single library update.

Actually, JSON seems to be a possible option, as it is "more structured" than tsv, and benchmarks shows pretty good parsing performance, at least for python/pandas...