Bio.HTS.Types

Documentation

newtype BAM

The BAM format.

Constructors

BAM

Fields

• unbam :: ForeignPtr Bam1

newtype BAMHeader

Constructors

BAMHeader

Fields

• unbamHeader :: ForeignPtr BamHdr

showBamHeader :: BAMHeader -> ByteString

data SortOrder

BAM sort order.

Constructors

Unknown

Unsorted

Queryname

Coordinate

Instances

Eq SortOrder

Defined in Bio.HTS.Types

Methods

(==) :: SortOrder -> SortOrder -> Bool

(/=) :: SortOrder -> SortOrder -> Bool

Show SortOrder

Defined in Bio.HTS.Types

Methods

showsPrec :: Int -> SortOrder -> ShowS

show :: SortOrder -> String

showList :: [SortOrder] -> ShowS

data SAM

The SAM format.

Constructors

SAM

Fields

• _sam_qname :: !ByteString
• _sam_flag :: !Word16
• _sam_rname :: !(Maybe ByteString)
• _sam_pos :: !Int
• _sam_mapq :: !Word8
• _sam_cigar :: !(Maybe [(Int, Char)])
• _sam_rnext :: !(Maybe ByteString)
• _sam_pnext :: !Int
• _sam_tlen :: !Int
• _sam_seq :: !(Maybe ByteString)
• _sam_qual :: !(Maybe ByteString)
• _sam_aux :: [((Char, Char), AuxiliaryData)]

data AuxiliaryData

Auxiliary data

Constructors

AuxChar Char

AuxInt Int

AuxFloat Float

AuxString ByteString

AuxByteArray ByteString

AuxIntArray [Int]

AuxFloatArray [Float]

Instances

Show AuxiliaryData

Defined in Bio.HTS.Types

Methods

showsPrec :: Int -> AuxiliaryData -> ShowS

show :: AuxiliaryData -> String

showList :: [AuxiliaryData] -> ShowS

showSam :: SAM -> ByteString