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#100 gatekeeper: fragment sampling

Gatekeeper
open
nobody
Feature (48)
5
2008-12-05
2008-12-05
Brian Walenz
No

Add sampling methods to allow:
-by library
-preserving mate/frag ratio
-only mated reads
-breaking mates (only way to get a mate pair is by picking both reads independently)

What is currently implemented is a small set of special cases. Is it possible to make this both simple and general?

-samplefrags -- pick reads independently
-samplemates -- pick mates independently
-includeunmated -- for -samplemates, also allow unmated reads

etc?

Discussion

  • Brian Walenz
    Brian Walenz
    2009-02-20

    In addition to "by library" also allow "over all fragments".