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ChangeLog.md

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CHANGED

  • All ID's, except external Fragment IDs, are now in one name space and every ID in a definitional context must be unique. External fragment IDs are in another name space. If * is specified in place of an ID on edge, gap, and group lines, then that item does not have an ID and is presumably not referred to elsewhere (i.e. U- or O-lines).

  • Sequences in S-lines were defined as [a-zA-Z]+. Unecessarily restrictive. Changed to any printable sequence excluding space, i.e [!-~]+.

  • There was some discussion about restricting headers to the first few lines, but in the end the consensus was to leave the specification free of any line order restrictions.

  • The P[UO]-line headers have been split into a U-line and an O-line.

  • A 'TS' SAM-tag in a header defines a default trace spacing to use with all traces, unless the line containing the trace has a 'TS' SAM-tag after the fixed fields specifying a spacing to use with that specific trace.

  • The README2.md and README.md have been consolidated into README.md.

  • The L-line extension has been removed.

  • X and = are removed from CIGAR strings, which are now restricted to MDIP.

  • The convention for positions has changed to Heng's proposal. Namely, a $ is now a sentinel that follows an integer position if and only if that position is the end of the segment. It will be considered an error for such a position not to be so marked. One can still test if an edge is a dovetail or containment because the $ effectively tells you the segment length.

  • The variance field in G-lines can now be either an integer or a * when not known.

  • In order to encompass all use-cases desired by the various parties, and to properly specify gap relationships, a mojority voted that references to objects are signed in those context where it makes sense and/or is necessary. An identifier followed by + or - is a signed-reference and orients the underlying segment, edge, or path accordingly. The sign is not a separate field but a post-fix mark on the identifier, analogous to the postfix $ on integer positions.

  • In regard to SAM-tags, only the 'VN' and 'TS' tags are explicitly in the specification and must be interpreted by applications. Two lists of optional tags will be maintained called the Core List and the Community List. The Core list will contain initially all GFA1 tags and any additions must be by community consensus. The Community list can more loosely contain any tags proposed by any user. The general expectation is that tags would initially be proposed on the community list, and if over time become popular, then could migrate to the core list.