#2 gff output - target in + strand coordinates

open
nobody
None
5
2012-12-13
2012-03-13
Anonymous
No

Changes gff output to always use + strand coordinates in the Target attribute (i.e. coords in the input sequence).

This is vaguely defined in the gff3 specification, but seems like more sensible thing to do, because neither the main coordinates in the gff file are inverted when the strand is -.

This also matches the behavior of gmap, which is handy when using output of those two mappers interchangeably.

Also contains a little fix escaping the == intron marks according to gff3 spec.

Discussion

  • Nobody/Anonymous

    unified diff (svn diff)

     
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    Anonymous - 2012-03-29

    Concentrating on the description I forgot to specify -- the patch is for sim4db.

     

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