Bio.Bam.Rec

Parsers and Printers for BAM and SAM.

Documentation

data BamRaw

Bam record in its native encoding along with virtual address.

Instances

IsBamRec BamRaw

Defined in Bio.Bam.Writer

Methods

pushBam :: BamRaw -> BgzfTokens -> BgzfTokens

unpackBamRec :: BamRaw -> BamRec

bamRaw :: MonadThrow m => Int64 -> Bytes -> m BamRaw

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

virt_offset :: BamRaw -> Int64

raw_data :: BamRaw -> Bytes

br_copy :: BamRaw -> BamRaw

data BamRec

More convenient representation of a BAM record. Invariant: Either b_qual == Nothing or fmap V.length b_qual == Just (V.length b_seq).

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 :: Maybe (Vector Qual)
• b_exts :: Extensions
• b_virtual_offset :: Int64

  virtual offset for indexing purposes

Instances

Show BamRec

Defined in Bio.Bam.Rec

Methods

showsPrec :: Int -> BamRec -> ShowS

show :: BamRec -> String

showList :: [BamRec] -> ShowS

IsBamRec BamRec

Defined in Bio.Bam.Writer

Methods

pushBam :: BamRec -> BgzfTokens -> BgzfTokens

unpackBamRec :: BamRec -> BamRec

unpackBam :: BamRaw -> BamRec

nullBamRec :: BamRec

getMd :: BamRec -> Maybe [MdOp]

data LengthMismatch

Constructors

LengthMismatch !Bytes

Instances

Show LengthMismatch

Defined in Bio.Bam.Rec

Methods

showsPrec :: Int -> LengthMismatch -> ShowS

show :: LengthMismatch -> String

showList :: [LengthMismatch] -> ShowS

Exception LengthMismatch

Defined in Bio.Bam.Rec

Methods

toException :: LengthMismatch -> SomeException

fromException :: SomeException -> Maybe LengthMismatch

displayException :: LengthMismatch -> String

data BrokenRecord

Constructors

BrokenRecord !Int [Int] !Bytes

Instances

Show BrokenRecord

Defined in Bio.Bam.Rec

Methods

showsPrec :: Int -> BrokenRecord -> ShowS

show :: BrokenRecord -> String

showList :: [BrokenRecord] -> ShowS

Exception BrokenRecord

Defined in Bio.Bam.Rec

Methods

toException :: BrokenRecord -> SomeException

fromException :: SomeException -> Maybe BrokenRecord

displayException :: BrokenRecord -> String

data Cigar

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

Defined in Bio.Bam.Rec

Methods

(==) :: Cigar -> Cigar -> Bool

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

Ord Cigar

Defined in Bio.Bam.Rec

Methods

compare :: Cigar -> Cigar -> Ordering

(<) :: Cigar -> Cigar -> Bool

(<=) :: Cigar -> Cigar -> Bool

(>) :: Cigar -> Cigar -> Bool

(>=) :: Cigar -> Cigar -> Bool

max :: Cigar -> Cigar -> Cigar

min :: Cigar -> Cigar -> Cigar

Show Cigar

Defined in Bio.Bam.Rec

Methods

showsPrec :: Int -> Cigar -> ShowS

show :: Cigar -> String

showList :: [Cigar] -> ShowS

Storable Cigar

Defined in Bio.Bam.Rec

Methods

sizeOf :: Cigar -> Int

alignment :: Cigar -> Int

peekElemOff :: Ptr Cigar -> Int -> IO Cigar

pokeElemOff :: Ptr Cigar -> Int -> Cigar -> IO ()

peekByteOff :: Ptr b -> Int -> IO Cigar

pokeByteOff :: Ptr b -> Int -> Cigar -> IO ()

peek :: Ptr Cigar -> IO Cigar

poke :: Ptr Cigar -> Cigar -> IO ()

data CigOp

Constructors

Mat

Ins

Del

Nop

SMa

HMa

Pad

Instances

Bounded CigOp

Defined in Bio.Bam.Rec

Methods

minBound :: CigOp

maxBound :: CigOp

Enum CigOp

Defined in Bio.Bam.Rec

Methods

succ :: CigOp -> CigOp

pred :: CigOp -> CigOp

toEnum :: Int -> CigOp

fromEnum :: CigOp -> Int

enumFrom :: CigOp -> [CigOp]

enumFromThen :: CigOp -> CigOp -> [CigOp]

enumFromTo :: CigOp -> CigOp -> [CigOp]

enumFromThenTo :: CigOp -> CigOp -> CigOp -> [CigOp]

Eq CigOp

Defined in Bio.Bam.Rec

Methods

(==) :: CigOp -> CigOp -> Bool

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

Ord CigOp

Defined in Bio.Bam.Rec

Methods

compare :: CigOp -> CigOp -> Ordering

(<) :: CigOp -> CigOp -> Bool

(<=) :: CigOp -> CigOp -> Bool

(>) :: CigOp -> CigOp -> Bool

(>=) :: CigOp -> CigOp -> Bool

max :: CigOp -> CigOp -> CigOp

min :: CigOp -> CigOp -> CigOp

Show CigOp

Defined in Bio.Bam.Rec

Methods

showsPrec :: Int -> CigOp -> ShowS

show :: CigOp -> String

showList :: [CigOp] -> ShowS

Ix CigOp

Defined in Bio.Bam.Rec

Methods

range :: (CigOp, CigOp) -> [CigOp]

index :: (CigOp, CigOp) -> CigOp -> Int

unsafeIndex :: (CigOp, CigOp) -> CigOp -> Int

inRange :: (CigOp, CigOp) -> CigOp -> Bool

rangeSize :: (CigOp, CigOp) -> Int

unsafeRangeSize :: (CigOp, CigOp) -> Int

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

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

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

Defined in Bio.Base

Methods

minBound :: Nucleotides

maxBound :: Nucleotides

Enum Nucleotides

Defined in Bio.Base

Methods

succ :: Nucleotides -> Nucleotides

pred :: Nucleotides -> Nucleotides

toEnum :: Int -> Nucleotides

fromEnum :: Nucleotides -> Int

enumFrom :: Nucleotides -> [Nucleotides]

enumFromThen :: Nucleotides -> Nucleotides -> [Nucleotides]

enumFromTo :: Nucleotides -> Nucleotides -> [Nucleotides]

enumFromThenTo :: Nucleotides -> Nucleotides -> Nucleotides -> [Nucleotides]

Eq Nucleotides

Defined in Bio.Base

Methods

(==) :: Nucleotides -> Nucleotides -> Bool

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

Ord Nucleotides

Defined in Bio.Base

Methods

compare :: Nucleotides -> Nucleotides -> Ordering

(<) :: Nucleotides -> Nucleotides -> Bool

(<=) :: Nucleotides -> Nucleotides -> Bool

(>) :: Nucleotides -> Nucleotides -> Bool

(>=) :: Nucleotides -> Nucleotides -> Bool

max :: Nucleotides -> Nucleotides -> Nucleotides

min :: Nucleotides -> Nucleotides -> Nucleotides

Read Nucleotides

Defined in Bio.Base

Methods

readsPrec :: Int -> ReadS Nucleotides

readList :: ReadS [Nucleotides]

readPrec :: ReadPrec Nucleotides

readListPrec :: ReadPrec [Nucleotides]

Show Nucleotides

Defined in Bio.Base

Methods

showsPrec :: Int -> Nucleotides -> ShowS

show :: Nucleotides -> String

showList :: [Nucleotides] -> ShowS

Ix Nucleotides

Defined in Bio.Base

Methods

range :: (Nucleotides, Nucleotides) -> [Nucleotides]

index :: (Nucleotides, Nucleotides) -> Nucleotides -> Int

unsafeIndex :: (Nucleotides, Nucleotides) -> Nucleotides -> Int

inRange :: (Nucleotides, Nucleotides) -> Nucleotides -> Bool

rangeSize :: (Nucleotides, Nucleotides) -> Int

unsafeRangeSize :: (Nucleotides, Nucleotides) -> Int

Semigroup Nucleotides

Defined in Bio.Base

Methods

(<>) :: Nucleotides -> Nucleotides -> Nucleotides

sconcat :: NonEmpty Nucleotides -> Nucleotides

stimes :: Integral b => b -> Nucleotides -> Nucleotides

Monoid Nucleotides

Defined in Bio.Base

Methods

mempty :: Nucleotides

mappend :: Nucleotides -> Nucleotides -> Nucleotides

mconcat :: [Nucleotides] -> Nucleotides

Storable Nucleotides

Defined in Bio.Base

Methods

sizeOf :: Nucleotides -> Int

alignment :: Nucleotides -> Int

peekElemOff :: Ptr Nucleotides -> Int -> IO Nucleotides

pokeElemOff :: Ptr Nucleotides -> Int -> Nucleotides -> IO ()

peekByteOff :: Ptr b -> Int -> IO Nucleotides

pokeByteOff :: Ptr b -> Int -> Nucleotides -> IO ()

peek :: Ptr Nucleotides -> IO Nucleotides

poke :: Ptr Nucleotides -> Nucleotides -> IO ()

Vector Vector_Nucs_half Nucleotides

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)

Defined in Bio.Bam.Rec

Methods

showsPrec :: Int -> Vector_Nucs_half Nucleotides -> ShowS

show :: Vector_Nucs_half Nucleotides -> String

showList :: [Vector_Nucs_half Nucleotides] -> ShowS

data Vector_Nucs_half a

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

Constructors

Vector_Nucs_half !Int !Int !(ForeignPtr Word8)

Instances

Vector Vector_Nucs_half Nucleotides

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)

Defined in Bio.Bam.Rec

Methods

showsPrec :: Int -> Vector_Nucs_half Nucleotides -> ShowS

show :: Vector_Nucs_half Nucleotides -> String

showList :: [Vector_Nucs_half Nucleotides] -> ShowS

type Mutable Vector_Nucs_half

Defined in Bio.Bam.Rec

type Mutable Vector_Nucs_half

type Extensions = [(BamKey, Ext)]

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

data Ext

Constructors

Int Int

Float Float

Text Bytes

Bin Bytes

Char Word8

IntArr (Vector Int)

FloatArr (Vector Float)

Instances

Eq Ext

Defined in Bio.Bam.Rec

Methods

(==) :: Ext -> Ext -> Bool

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

Ord Ext

Defined in Bio.Bam.Rec

Methods

compare :: Ext -> Ext -> Ordering

(<) :: Ext -> Ext -> Bool

(<=) :: Ext -> Ext -> Bool

(>) :: Ext -> Ext -> Bool

(>=) :: Ext -> Ext -> Bool

max :: Ext -> Ext -> Ext

min :: Ext -> Ext -> Ext

Show Ext

Defined in Bio.Bam.Rec

Methods

showsPrec :: Int -> Ext -> ShowS

show :: Ext -> String

showList :: [Ext] -> ShowS

extAsInt :: Int -> BamKey -> BamRec -> Int

extAsString :: BamKey -> BamRec -> Bytes

setQualFlag :: Char -> BamRec -> BamRec

deleteE :: BamKey -> Extensions -> Extensions

Deletes all occurences of some extension field.

insertE :: BamKey -> Ext -> Extensions -> Extensions

Blindly inserts an extension field. This can create duplicates (and there is no telling how other tools react to that).

updateE :: BamKey -> Ext -> Extensions -> Extensions

Deletes all occurences of an extension field, then inserts it with a new value. This is safer than insertE, but also more expensive.

adjustE :: (Ext -> Ext) -> BamKey -> Extensions -> Extensions

Adjusts a named extension by applying a function.

isPaired :: BamRec -> Bool

isProperlyPaired :: BamRec -> Bool

isUnmapped :: BamRec -> Bool

isMateUnmapped :: BamRec -> Bool

isReversed :: BamRec -> Bool

isMateReversed :: BamRec -> Bool

isFirstMate :: BamRec -> Bool

isSecondMate :: 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