|
|
|
|
|
| Description |
| This implements a number of filters used in the Titanium pipeline
|
|
| Synopsis |
|
|
|
|
| Discarding filters **
|
|
|
| DiscardFilters determine whether a read is to be retained or discarded
|
|
|
|
|
|
|
|
|
|
|
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 **
|
|
|
| TrimFilters modify the read, typically trimming it for quality
|
|
|
|
|
|
|
| 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).
|
|
|
| 3.2.2.1.7 Quality score trimming trims using a 10-base window until a Q20 average is found.
|
|
| Utility functions **
|
|
|
| List length as a double (eliminates many instances of fromIntegral)
|
|
|
| Calculate average of a list
|
|
|
| Translate a number of flows to position in sequence, and update clipping data accordingly
|
|
|
| Update clip_qual_right if more severe than previous value
|
|
| Produced by Haddock version 2.6.1 |
