Biobase.MAF
Description
MAF, multiple alignment format provides multiple alignments with genome-wide scale. Often used for n-way alignments with n genomes aligned against one reference genome.
We follow http://genome.ucsc.edu/FAQ/FAQformat.html#format5
TODO this is not a complete implementation of the MAF format
- data MAF = MAF {
- mafheader :: KVs
- comments :: [ByteString]
- metadata :: [ByteString]
- blocks :: [Alignment]
- data Alignment = Alignment {}
- type KVs = Map ByteString ByteString
- data Aligned = Aligned {
- key :: ByteString
- start :: Int
- length :: Int
- strand :: Char
- genomesize :: Int
- value :: ByteString
Documentation
The header of a MAF file. Reads the initial lines beginning with '#'.
Constructors
| MAF | |
Fields
| |
Each alignment.
type KVs = Map ByteString ByteStringSource
Some key-value pairs are defined; these are in a map
a single aligned sequence.
TODO this should later on be a BioSeq (cf. Ketil Maldes work) but that change stays in an experimental repo until BioSeq is available on hackage
Constructors
| Aligned | |
Fields
| |