Safe Haskell | None |
---|---|
Language | Haskell2010 |
Synopsis
- class Cleanable a where
- clean :: a -> Maybe a
- cleanWith :: Thresholds -> a -> Maybe a
- data Thresholds = Thresholds {}
Documentation
class Cleanable a where Source #
Ability to clean initial data.
Returns cleaned variant or Nothing
if it can not be cleaned.
Instances
Cleanable BasecalledSequence Source # | |
Defined in Bio.ABI.Clean |
data Thresholds Source #
Thresholds to clean the data. ABI file contains sequence with quality. By design of sanger sequencing method start and end of the sequence have bad quality. Moreover, internal part of the sequence can also has bad quality. To clean the data we make 2 steps.
Step 1. Clean edges:
* take frame with frameSize
and go through the sequence;
* on each step evaluate mean value;
* if mean value less than edgeThreshold
, go further;
* if mean value more than edgeThreshold
, stop and cut the sequence from END of this frame;
* repeat this algorithm for the right edge.
Step 2. Evaluate quality:
* for cropped sequence evaluate mean value;
* if mean value less then innerThreshold
, sequence is bad;
* if mean value more then innerThreshold
, sequence is acceptable.
Logic of this algorithm and defaultThresholds
were obtained by taking experiments with read ABI files.
Instances
Eq Thresholds Source # | |
Defined in Bio.ABI.Clean (==) :: Thresholds -> Thresholds -> Bool # (/=) :: Thresholds -> Thresholds -> Bool # | |
Show Thresholds Source # | |
Defined in Bio.ABI.Clean showsPrec :: Int -> Thresholds -> ShowS # show :: Thresholds -> String # showList :: [Thresholds] -> ShowS # |