Bio.HTS.Types

Documentation

htsCtx :: Context

newtype BamFileHandle

Constructors

BamFileHandle (Ptr HTSFile)

data FileHeader

Constructors

Empty

BamHeader (Ptr BamHdr)

data BamHdr

data HTSFile

type Bam = ForeignPtr Bam'

data Bam'

data Sam

currently only contains 11 mandatory fields

Constructors

Sam

Fields

• samQname :: !ByteString
• samFlag :: !Word16
• samRname :: !(Maybe ByteString)
• samPos :: !Int32
• samMapq :: !Word8
• samCigar :: !(Maybe [(Int, Char)])
• samRnext :: !(Maybe ByteString)
• samPnext :: !Int32
• samTlen :: !Int32
• samSeq :: !(Maybe ByteString)
• samQual :: !(Maybe ByteString)

Instances

Show Sam

Methods

showsPrec :: Int -> Sam -> ShowS

show :: Sam -> String

showList :: [Sam] -> ShowS

newtype Flag

SAM record flag

Constructors

Flag Word16

showSam :: Sam -> ByteString