Safe Haskell	None
Language	Haskell2010

Bio.Bam.Rec

Description

Parsers and Printers for BAM and SAM.

Synopsis

data BamRaw
bamRaw :: Int64 -> Bytes -> BamRaw
virt_offset :: BamRaw -> Int64
raw_data :: BamRaw -> Bytes
data BamRec = BamRec {
- b_qname :: Bytes
- b_flag :: Int
- b_rname :: Refseq
- b_pos :: Int
- b_mapq :: Qual
- b_cigar :: Vector Cigar
- b_mrnm :: Refseq
- b_mpos :: Int
- b_isize :: Int
- b_seq :: Vector_Nucs_half Nucleotides
- b_qual :: Vector Qual
- b_exts :: Extensions
- b_virtual_offset :: Int64
}
unpackBam :: BamRaw -> BamRec
nullBamRec :: BamRec
getMd :: BamRec -> Maybe [MdOp]
data Cigar = !CigOp :* !Int
data CigOp
- = Mat
- | Ins
- | Del
- | Nop
- | SMa
- | HMa
- | Pad
alignedLength :: Vector v Cigar => v Cigar -> Int
newtype Nucleotides = Ns {
- unNs :: Word8
}
data Vector_Nucs_half a
type Extensions = [(BamKey, Ext)]
data Ext
- = Int Int
- | Float Float
- | Text Bytes
- | Bin Bytes
- | Char Word8
- | IntArr (Vector Int)
- | FloatArr (Vector Float)
extAsInt :: Int -> BamKey -> BamRec -> Int
extAsString :: BamKey -> BamRec -> Bytes
setQualFlag :: Char -> BamRec -> BamRec
deleteE :: BamKey -> Extensions -> Extensions
insertE :: BamKey -> Ext -> Extensions -> Extensions
updateE :: BamKey -> Ext -> Extensions -> Extensions
adjustE :: (Ext -> Ext) -> BamKey -> Extensions -> Extensions
isPaired :: BamRec -> Bool
isProperlyPaired :: BamRec -> Bool
isUnmapped :: BamRec -> Bool
isMateUnmapped :: BamRec -> Bool
isReversed :: BamRec -> Bool
isMateReversed :: BamRec -> Bool
isFirstMate :: BamRec -> Bool
isSecondMate :: BamRec -> Bool
isAuxillary :: BamRec -> Bool
isSecondary :: BamRec -> Bool
isFailsQC :: BamRec -> Bool
isDuplicate :: BamRec -> Bool
isSupplementary :: BamRec -> Bool
isTrimmed :: BamRec -> Bool
isMerged :: BamRec -> Bool
isAlternative :: BamRec -> Bool
isExactIndex :: BamRec -> Bool
type_mask :: Int

Documentation

data BamRaw Source #

Bam record in its native encoding along with virtual address.

Instances

IsBamRec BamRaw Source #
Instance details Defined in Bio.Bam.Writer Methods pushBam :: BamRaw -> BgzfTokens -> BgzfTokens Source # unpackBamRec :: BamRaw -> BamRec Source #

bamRaw :: Int64 -> Bytes -> BamRaw Source #

Smart constructor. Makes sure we got a at least a full record.

virt_offset :: BamRaw -> Int64 Source #

raw_data :: BamRaw -> Bytes Source #

data BamRec Source #

internal representation of a BAM record

Constructors

BamRec
Fields b_qname :: Bytes b_flag :: Int b_rname :: Refseq b_pos :: Int b_mapq :: Qual b_cigar :: Vector Cigar b_mrnm :: Refseq b_mpos :: Int b_isize :: Int b_seq :: Vector_Nucs_half Nucleotides b_qual :: Vector Qual b_exts :: Extensions b_virtual_offset :: Int64 virtual offset for indexing purposes

Instances

Show BamRec Source #
Instance details Defined in Bio.Bam.Rec Methods showsPrec :: Int -> BamRec -> ShowS Source # show :: BamRec -> String Source # showList :: [BamRec] -> ShowS Source #
IsBamRec BamRec Source #
Instance details Defined in Bio.Bam.Writer Methods pushBam :: BamRec -> BgzfTokens -> BgzfTokens Source # unpackBamRec :: BamRec -> BamRec Source #

unpackBam :: BamRaw -> BamRec Source #

nullBamRec :: BamRec Source #

getMd :: BamRec -> Maybe [MdOp] Source #

data Cigar Source #

Cigar line in BAM coding Bam encodes an operation and a length into a single integer, we keep those integers in an array.

Constructors

!CigOp :* !Int infix 9

Instances

Eq Cigar Source #
Instance details Defined in Bio.Bam.Rec Methods (==) :: Cigar -> Cigar -> Bool Source # (/=) :: Cigar -> Cigar -> Bool Source #
Ord Cigar Source #
Instance details Defined in Bio.Bam.Rec Methods compare :: Cigar -> Cigar -> Ordering Source # (<) :: Cigar -> Cigar -> Bool Source # (<=) :: Cigar -> Cigar -> Bool Source # (>) :: Cigar -> Cigar -> Bool Source # (>=) :: Cigar -> Cigar -> Bool Source # max :: Cigar -> Cigar -> Cigar Source # min :: Cigar -> Cigar -> Cigar Source #
Show Cigar Source #
Instance details Defined in Bio.Bam.Rec Methods showsPrec :: Int -> Cigar -> ShowS Source # show :: Cigar -> String Source # showList :: [Cigar] -> ShowS Source #
Storable Cigar Source #
Instance details Defined in Bio.Bam.Rec Methods sizeOf :: Cigar -> Int Source # alignment :: Cigar -> Int Source # peekElemOff :: Ptr Cigar -> Int -> IO Cigar Source # pokeElemOff :: Ptr Cigar -> Int -> Cigar -> IO () Source # peekByteOff :: Ptr b -> Int -> IO Cigar Source # pokeByteOff :: Ptr b -> Int -> Cigar -> IO () Source # peek :: Ptr Cigar -> IO Cigar Source # poke :: Ptr Cigar -> Cigar -> IO () Source #

data CigOp Source #

Constructors

Mat
Ins
Del
Nop
SMa
HMa
Pad

Instances

Bounded CigOp Source #
Instance details Defined in Bio.Bam.Rec Methods minBound :: CigOp Source # maxBound :: CigOp Source #
Enum CigOp Source #
Instance details Defined in Bio.Bam.Rec Methods succ :: CigOp -> CigOp Source # pred :: CigOp -> CigOp Source # toEnum :: Int -> CigOp Source # fromEnum :: CigOp -> Int Source # enumFrom :: CigOp -> [CigOp] Source # enumFromThen :: CigOp -> CigOp -> [CigOp] Source # enumFromTo :: CigOp -> CigOp -> [CigOp] Source # enumFromThenTo :: CigOp -> CigOp -> CigOp -> [CigOp] Source #
Eq CigOp Source #
Instance details Defined in Bio.Bam.Rec Methods (==) :: CigOp -> CigOp -> Bool Source # (/=) :: CigOp -> CigOp -> Bool Source #
Ord CigOp Source #
Instance details Defined in Bio.Bam.Rec Methods compare :: CigOp -> CigOp -> Ordering Source # (<) :: CigOp -> CigOp -> Bool Source # (<=) :: CigOp -> CigOp -> Bool Source # (>) :: CigOp -> CigOp -> Bool Source # (>=) :: CigOp -> CigOp -> Bool Source # max :: CigOp -> CigOp -> CigOp Source # min :: CigOp -> CigOp -> CigOp Source #
Show CigOp Source #
Instance details Defined in Bio.Bam.Rec Methods showsPrec :: Int -> CigOp -> ShowS Source # show :: CigOp -> String Source # showList :: [CigOp] -> ShowS Source #
Ix CigOp Source #
Instance details Defined in Bio.Bam.Rec Methods range :: (CigOp, CigOp) -> [CigOp] Source # index :: (CigOp, CigOp) -> CigOp -> Int Source # unsafeIndex :: (CigOp, CigOp) -> CigOp -> Int inRange :: (CigOp, CigOp) -> CigOp -> Bool Source # rangeSize :: (CigOp, CigOp) -> Int Source # unsafeRangeSize :: (CigOp, CigOp) -> Int

alignedLength :: Vector v Cigar => v Cigar -> Int Source #

Extracts the aligned length from a cigar line. This gives the length of an alignment as measured on the reference, which is different from the length on the query or the length of the alignment.

newtype Nucleotides Source #

A nucleotide base in an alignment. Experience says we're dealing with Ns and gaps all the type, so purity be damned, they are included as if they were real bases.

To allow Nucleotidess to be unpacked and incorporated into containers, we choose to represent them the same way as the BAM file format: as a 4 bit wide field. Gaps are encoded as 0 where they make sense, N is 15. The contained Word8 is guaranteed to be 0..15.

Constructors

Ns
Fields unNs :: Word8

Instances

Bounded Nucleotides Source #
Instance details Defined in Bio.Base Methods minBound :: Nucleotides Source # maxBound :: Nucleotides Source #
Enum Nucleotides Source #
Instance details Defined in Bio.Base Methods succ :: Nucleotides -> Nucleotides Source # pred :: Nucleotides -> Nucleotides Source # toEnum :: Int -> Nucleotides Source # fromEnum :: Nucleotides -> Int Source # enumFrom :: Nucleotides -> [Nucleotides] Source # enumFromThen :: Nucleotides -> Nucleotides -> [Nucleotides] Source # enumFromTo :: Nucleotides -> Nucleotides -> [Nucleotides] Source # enumFromThenTo :: Nucleotides -> Nucleotides -> Nucleotides -> [Nucleotides] Source #
Eq Nucleotides Source #
Instance details Defined in Bio.Base Methods (==) :: Nucleotides -> Nucleotides -> Bool Source # (/=) :: Nucleotides -> Nucleotides -> Bool Source #
Ord Nucleotides Source #
Instance details Defined in Bio.Base Methods compare :: Nucleotides -> Nucleotides -> Ordering Source # (<) :: Nucleotides -> Nucleotides -> Bool Source # (<=) :: Nucleotides -> Nucleotides -> Bool Source # (>) :: Nucleotides -> Nucleotides -> Bool Source # (>=) :: Nucleotides -> Nucleotides -> Bool Source # max :: Nucleotides -> Nucleotides -> Nucleotides Source # min :: Nucleotides -> Nucleotides -> Nucleotides Source #
Read Nucleotides Source #
Instance details Defined in Bio.Base Methods readsPrec :: Int -> ReadS Nucleotides Source # readList :: ReadS [Nucleotides] Source # readPrec :: ReadPrec Nucleotides Source # readListPrec :: ReadPrec [Nucleotides] Source #
Show Nucleotides Source #
Instance details Defined in Bio.Base Methods showsPrec :: Int -> Nucleotides -> ShowS Source # show :: Nucleotides -> String Source # showList :: [Nucleotides] -> ShowS Source #
Ix Nucleotides Source #
Instance details Defined in Bio.Base Methods range :: (Nucleotides, Nucleotides) -> [Nucleotides] Source # index :: (Nucleotides, Nucleotides) -> Nucleotides -> Int Source # unsafeIndex :: (Nucleotides, Nucleotides) -> Nucleotides -> Int inRange :: (Nucleotides, Nucleotides) -> Nucleotides -> Bool Source # rangeSize :: (Nucleotides, Nucleotides) -> Int Source # unsafeRangeSize :: (Nucleotides, Nucleotides) -> Int
Storable Nucleotides Source #
Instance details Defined in Bio.Base Methods sizeOf :: Nucleotides -> Int Source # alignment :: Nucleotides -> Int Source # peekElemOff :: Ptr Nucleotides -> Int -> IO Nucleotides Source # pokeElemOff :: Ptr Nucleotides -> Int -> Nucleotides -> IO () Source # peekByteOff :: Ptr b -> Int -> IO Nucleotides Source # pokeByteOff :: Ptr b -> Int -> Nucleotides -> IO () Source # peek :: Ptr Nucleotides -> IO Nucleotides Source # poke :: Ptr Nucleotides -> Nucleotides -> IO () Source #
Vector Vector_Nucs_half Nucleotides
Instance details Defined in Bio.Bam.Rec Methods basicUnsafeFreeze :: PrimMonad m => Mutable Vector_Nucs_half (PrimState m) Nucleotides -> m (Vector_Nucs_half Nucleotides) basicUnsafeThaw :: PrimMonad m => Vector_Nucs_half Nucleotides -> m (Mutable Vector_Nucs_half (PrimState m) Nucleotides) basicLength :: Vector_Nucs_half Nucleotides -> Int basicUnsafeSlice :: Int -> Int -> Vector_Nucs_half Nucleotides -> Vector_Nucs_half Nucleotides basicUnsafeIndexM :: Monad m => Vector_Nucs_half Nucleotides -> Int -> m Nucleotides basicUnsafeCopy :: PrimMonad m => Mutable Vector_Nucs_half (PrimState m) Nucleotides -> Vector_Nucs_half Nucleotides -> m () elemseq :: Vector_Nucs_half Nucleotides -> Nucleotides -> b -> b
Show (Vector_Nucs_half Nucleotides) Source #
Instance details Defined in Bio.Bam.Rec Methods showsPrec :: Int -> Vector_Nucs_half Nucleotides -> ShowS Source # show :: Vector_Nucs_half Nucleotides -> String Source # showList :: [Vector_Nucs_half Nucleotides] -> ShowS Source #

data Vector_Nucs_half a Source #

A vector that packs two Nucleotides into one byte, just like Bam does.

Instances

Vector Vector_Nucs_half Nucleotides Source #
Instance details Defined in Bio.Bam.Rec Methods basicUnsafeFreeze :: PrimMonad m => Mutable Vector_Nucs_half (PrimState m) Nucleotides -> m (Vector_Nucs_half Nucleotides) basicUnsafeThaw :: PrimMonad m => Vector_Nucs_half Nucleotides -> m (Mutable Vector_Nucs_half (PrimState m) Nucleotides) basicLength :: Vector_Nucs_half Nucleotides -> Int basicUnsafeSlice :: Int -> Int -> Vector_Nucs_half Nucleotides -> Vector_Nucs_half Nucleotides basicUnsafeIndexM :: Monad m => Vector_Nucs_half Nucleotides -> Int -> m Nucleotides basicUnsafeCopy :: PrimMonad m => Mutable Vector_Nucs_half (PrimState m) Nucleotides -> Vector_Nucs_half Nucleotides -> m () elemseq :: Vector_Nucs_half Nucleotides -> Nucleotides -> b -> b
Show (Vector_Nucs_half Nucleotides) Source #
Instance details Defined in Bio.Bam.Rec Methods showsPrec :: Int -> Vector_Nucs_half Nucleotides -> ShowS Source # show :: Vector_Nucs_half Nucleotides -> String Source # showList :: [Vector_Nucs_half Nucleotides] -> ShowS Source #
type Mutable Vector_Nucs_half Source #
Instance details Defined in Bio.Bam.Rec type Mutable Vector_Nucs_half

type Extensions = [(BamKey, Ext)] Source #

A collection of extension fields. A BamKey is actually two ASCII characters.

data Ext Source #

Constructors

Int Int
Float Float
Text Bytes
Bin Bytes
Char Word8
IntArr (Vector Int)
FloatArr (Vector Float)

Instances

Eq Ext Source #
Instance details Defined in Bio.Bam.Rec Methods (==) :: Ext -> Ext -> Bool Source # (/=) :: Ext -> Ext -> Bool Source #
Ord Ext Source #
Instance details Defined in Bio.Bam.Rec Methods compare :: Ext -> Ext -> Ordering Source # (<) :: Ext -> Ext -> Bool Source # (<=) :: Ext -> Ext -> Bool Source # (>) :: Ext -> Ext -> Bool Source # (>=) :: Ext -> Ext -> Bool Source # max :: Ext -> Ext -> Ext Source # min :: Ext -> Ext -> Ext Source #
Show Ext Source #
Instance details Defined in Bio.Bam.Rec Methods showsPrec :: Int -> Ext -> ShowS Source # show :: Ext -> String Source # showList :: [Ext] -> ShowS Source #