| bio-0.4.6: A bioinformatics library | Source code | Contents | Index
Bio.Sequence.SFF_filters
Contents
Discarding filters ** Trimming filters ** Utility functions **
Description
This implements a number of filters used in the Titanium pipeline
Synopsis
type DiscardFilter = ReadBlock -> Bool
filter_mixed :: DiscardFilter
filter_key :: DiscardFilter
filter_empty :: DiscardFilter
filter_dots :: DiscardFilter
filter_length :: Int -> DiscardFilter
type TrimFilter = ReadBlock -> ReadBlock
filter_qual20 :: TrimFilter
filter_sigint :: TrimFilter
sigint :: ReadBlock -> Int
qual20 :: ReadBlock -> Int
dlength :: [a] -> Double
avg :: Integral a => [a] -> Double
clipFlows :: ReadBlock -> Int -> ReadBlock
clipSeq :: ReadBlock -> Int -> ReadBlock
Discarding filters **
type DiscardFilter = ReadBlock -> Bool | Source
DiscardFilters determine whether a read is to be retained or discarded
filter_mixed :: DiscardFilter | Source
filter_key :: DiscardFilter | Source
filter_empty :: DiscardFilter | Source
filter_dots :: DiscardFilter | Source
filter_length :: Int -> DiscardFilter | Source
3.2.2.1.2 The dots filter discards sequences where the last positive flow is before flow 84, and flows with >5% dots (i.e. three successive noise values) before the last postitive flow. (Interpreted as 5% of called sequence length is Ns?) 3.2.2.1.3 The mixed filter discards sequences with more than 70% positive flows. Also, discard with 30% noise, 20% middle (0.45..0.75) or <30% positive. Discard a read if the number of untrimmed flows is less than n (n=186 for Titanium)
Trimming filters **
type TrimFilter = ReadBlock -> ReadBlock | Source
TrimFilters modify the read, typically trimming it for quality
filter_qual20 :: TrimFilter | Source
filter_sigint :: TrimFilter | Source
sigint :: ReadBlock -> Int | Source
3.2.2.1.4 Signal intensity trim - trim back until <3% borderline flows (0.5..0.7). Then trim borderline values or dots from the end (use a window).
qual20 :: ReadBlock -> Int | Source
3.2.2.1.7 Quality score trimming trims using a 10-base window until a Q20 average is found.
Utility functions **
dlength :: [a] -> Double | Source
List length as a double (eliminates many instances of fromIntegral)
avg :: Integral a => [a] -> Double | Source
Calculate average of a list
clipFlows :: ReadBlock -> Int -> ReadBlock | Source
Translate a number of flows to position in sequence, and update clipping data accordingly
clipSeq :: ReadBlock -> Int -> ReadBlock | Source
Update clip_qual_right if more severe than previous value
Produced by Haddock version 2.4.2