| bio-0.4.6: A bioinformatics library | Source code | Contents | Index
Bio.Alignment.BED
Description
Model the BED format, according to the spec at http:genome.ucsc.eduFAQFAQformat#format1
Synopsis
data BED = BED {
chrom :: ByteString
chromStart :: Offset
chromEnd :: Offset
name :: ByteString
score :: Int
strand :: Dir
thickStart :: Offset
thickEnd :: Offset
itemRGB :: (Word8, Word8, Word8)
blockSizeStart :: [(Offset, Offset)]
}
data Dir
= Fwd
| Rev
readBED :: FilePath -> IO [BED]
writeBED :: FilePath -> [BED] -> IO ()
Documentation
data BED | Source
The BED data type Note that the specification allows a variable number of fields, with only the three first required. This definition requires all fields to be present.
Constructors
BED |
chrom :: ByteString |
chromStart :: Offset |
chromEnd :: Offset |
name :: ByteString |
score :: Int | Range 0..1000
strand :: Dir |
thickStart :: Offset |
thickEnd :: Offset |
itemRGB :: (Word8, Word8, Word8) | Available BED files appear to not support this format. RGB is therefore ignored (read and written as '0')
blockSizeStart :: [(Offset, Offset)] | Lists of lenght blockCount, blockStarts are relative to chromStart
Instances
Show BED
data Dir | Source
Yet another direction data structure.
Constructors
Fwd |
Rev |
Instances
Eq Dir
Read Dir
Show Dir
readBED :: FilePath -> IO [BED] | Source
writeBED :: FilePath -> [BED] -> IO () | Source
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