Bio.Bam.Rec

Parsers and Printers for BAM and SAM. We employ an Iteratee interface, and we strive to support everything possible in BAM. So far, the implementation of the nucleotides is somewhat lacking: we do not have support for ambiguity codes, and the "=" symbol is not understood.

Documentation

data BamRaw

Bam record in its native encoding along with virtual address.

Instances

IsBamRec BamRaw

bamRaw :: FileOffset -> ByteString -> BamRaw

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

virt_offset :: BamRaw -> FileOffset

raw_data :: BamRaw -> ByteString

data BamRec

internal representation of a BAM record

Constructors

BamRec

Fields

b_qname :: Seqid

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 :: FileOffset

virtual offset for indexing purposes

Instances

Show BamRec

IsBamRec BamRec

unpackBam :: BamRaw -> BamRec

nullBamRec :: BamRec

getMd :: BamRec -> Maybe [MdOp]

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

Ord Cigar

Show Cigar

Storable Cigar

data CigOp

Constructors

Mat

Ins

Del

Nop

SMa

HMa

Pad

Instances

Bounded CigOp

Enum CigOp

Eq CigOp

Ord CigOp

Show CigOp

Ix CigOp

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 incorparated 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.

Constructors

Ns

Fields

unNs :: Word8

Instances

Bounded Nucleotides

Enum Nucleotides

Eq Nucleotides

Ord Nucleotides

Read Nucleotides

Show Nucleotides

Ix Nucleotides

Storable Nucleotides

Unbox Nucleotides

Vector Vector Nucleotides

Vector Vector_Nucs_half Nucleotides

MVector MVector Nucleotides

Show (Vector_Nucs_half Nucleotides)

data Vector Nucleotides = V_Nucleotides (Vector Word8)

data MVector s0 Nucleotides = MV_Nucleotides (MVector s Word8)

data Vector_Nucs_half a

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

Instances

Vector Vector_Nucs_half Nucleotides

Show (Vector_Nucs_half Nucleotides)

type Mutable Vector_Nucs_half

type Extensions = [(BamKey, Ext)]

A collection of extension fields. The key is actually only two Chars, but that proved impractical. (Hmm... we could introduce a Key type that is a 16 bit int, then give it an instance IsString... practical?)

data Ext

Constructors

Int Int

Float Float

Text ByteString

Bin ByteString

Char Word8

IntArr (Vector Int)

FloatArr (Vector Float)

Instances

Eq Ext

Ord Ext

Show Ext

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

extAsString :: BamKey -> BamRec -> ByteString

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

isAuxillary :: BamRec -> Bool

isFailsQC :: BamRec -> Bool

isDuplicate :: BamRec -> Bool

isTrimmed :: BamRec -> Bool

isMerged :: BamRec -> Bool

type_mask :: Int

progressPos :: MonadIO m => String -> (String -> IO ()) -> Refs -> Enumeratee [BamRaw] [BamRaw] m a

A simple progress indicator that prints sequence id and position.

data Word32 :: *

32-bit unsigned integer type

Instances

Bounded Word32

Enum Word32

Eq Word32

Integral Word32

Num Word32

Ord Word32

Read Word32

Real Word32

Show Word32

Ix Word32

Storable Word32

Bits Word32

FiniteBits Word32

Binary Word32

Hashable Word32

Prim Word32

Random Word32

Lift Word32

Unbox Word32

IArray UArray Word32

Vector Vector Word32

MVector MVector Word32

ReadableChunk [Word32] Word32

MArray (STUArray s) Word32 (ST s)

data Vector Word32 = V_Word32 (Vector Word32)

data MVector s Word32 = MV_Word32 (MVector s Word32)