| Safe Haskell | None |
|---|---|
| Language | Haskell98 |
Bio.Bam.Trim
Description
Trimming of reads as found in BAM files. Implements trimming low quality sequence from the 3' end.
Documentation
trim_3' :: ([Nucleotides] -> [Qual] -> Bool) -> BamRec -> BamRec Source
Trims from the 3' end of a sequence.
trim_3' p b trims the 3' end of the sequence in b at the
earliest position such that p evaluates to true on every suffix
that was trimmed off. Note that the 3' end may be the beginning of
the sequence if it happens to be stored in reverse-complemented form.
Also note that trimming from the 3' end may not make sense for reads
that were constructed by merging paired end data (but we cannot take
care of that here). Further note that trimming may break dependent
information, notably the "mate" information of the mate and many
optional fields.
TODO: The MD field is currently removed. It should be repaired instead. Many other fields should be trimmed if present.
trim_low_quality :: Qual -> a -> [Qual] -> Bool Source
Trim predicate to get rid of low quality sequence.
trim_low_quality q ns qs evaluates to true if all qualities in qs
are smaller (i.e. worse) than q.