Added optional SC tag to GFA2, similar to GFA1.2 + readme update #116
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…ification for cuts in segments As discussed today with @lh3, I am proposing to allow optional specification of subsequences directly in a path component, e.g. e.g. ptg000124l.1(397101:505533)+ We have devised a new tool (gfastats) that can take an agp file, for example from a scaffolding tool, and overlay the information on the original graph. When cuts are made within contigs, the segment is unmutable but we represent this event with coordinates associated to the component in the path, allowing to easily identify where cuts have occurred in the original segments
Some discussion points marked by TODO
Addressing comments by @asl, no more TODOs
Addressing comments by @lh3
Misprint fix
Fix SC tag
Based on the specifications of GFA1.2, a tag is added to indicate specific shortcut connections of assembly scaffolds (as opposed to missed overlaps or missing sequence during graph construction)
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Based on a discussion with @snurk it seems useful to ensure the presence of a tag to specify shortcut connections among the possible types of gap lines