bio-0.5.3: A bioinformatics library

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Bio.Alignment.BED

Description

Model the BED format, according to the spec at http:genome.ucsc.eduFAQFAQformat#format1

Synopsis

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 

Fields

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

data Dir Source

Yet another direction data structure.

Constructors

Fwd 
Rev 

Instances