bio-0.5.3: A bioinformatics library

Safe HaskellSafe
LanguageHaskell98

Bio.Alignment.BED

Description

Model the BED format, according to the spec at http://genome.ucsc.edu/FAQ/FAQformat#format1

Synopsis

Documentation

data BED

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 

Fields

chrom :: ByteString
 
chromStart, chromEnd :: Offset
 
name :: ByteString
 
score :: Int

Range 0..1000

strand :: Dir
 
thickStart, 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

data Dir

Yet another direction data structure.

Constructors

Fwd 
Rev 

Instances

writeBED :: FilePath -> [BED] -> IO ()