Data.BAM.Version1_6.BAM.Alignment.Base

Description

This library enables the decoding/encoding of SAM, BAM and CRAM file formats.

BAM version 1.6 alignment mandatory and optional data types

data BAM_V1_6_BAM_Alignment

Custom BAM (version 1.6) BAM_V1_6_BAM_Alignment data type.

See section 4.2 of the SAM v1.6 specification documentation.

Constructors

BAM_V1_6_BAM_Alignment

Fields

• bam_v1_6_bam_alignment_block_size :: Word32

  Total length of the alignment record, excluding this field.

• bam_v1_6_bam_alignment_refID :: Int32

  Reference sequence ID, -1 <= refID <= n_ref; -1 for a read without a mapping position.

• bam_v1_6_bam_alignment_pos :: Int32

  0-based leftmost coordinate (= POS - 1).

• bam_v1_6_bam_alignment_l_read_name :: Word8

  Length of read_name below (= length(QNAME) + 1).

• bam_v1_6_bam_alignment_mapq :: Word8

  Mapping quality (= MAPQ).

• bam_v1_6_bam_alignment_bin :: Word16

  BAI index bin, see Section 4.2.1.

• bam_v1_6_bam_alignment_n_cigar_op :: Word16

  Number of operations in CIGAR, see section 4.2.2.

• bam_v1_6_bam_alignment_flag :: Word16

  Bitwise flags (= FLAG).

• bam_v1_6_bam_alignment_l_seq :: Word32

  Length of SEQ.

• bam_v1_6_bam_alignment_next_refID :: Int32

  Ref-ID of the next seqment (-1 <= next_refID <= n_ref).

• bam_v1_6_bam_alignment_next_pos :: Int32

  0-based leftmost pos of the next segment (= PNEXT - 1).

• bam_v1_6_bam_alignment_tlen :: Int32

  Template length (= TLEN).

• bam_v1_6_bam_alignment_read_name :: ByteString

  Read name; NUL-terminated (QNAME with trailing 0x00/'0').

• bam_v1_6_bam_alignment_cigar :: Seq Word32

  CIGAR; op_len<<4<<|op. 'MIDNSHP=X' -> '012345678'.

• bam_v1_6_bam_alignment_seq :: Seq Word8

  4-bit encoded read: '=ACMGRSVTWYHKDBN' -> [0,15]. See section 4.2.3.

• bam_v1_6_bam_alignment_qual :: ByteString

  Phred-scaled base qualities. See section 4.2.3.

• bam_v1_6_bam_alignment_optionalfields :: Seq BAM_V1_6_BAM_Alignment_OptionalFields

  List of auxiliary data. See section 4.2.4

Instances

Generic BAM_V1_6_BAM_Alignment

Defined in Data.BAM.Version1_6.BAM.Alignment.Base

Associated Types

type Rep BAM_V1_6_BAM_Alignment :: Type -> Type

Methods

from :: BAM_V1_6_BAM_Alignment -> Rep BAM_V1_6_BAM_Alignment x

to :: Rep BAM_V1_6_BAM_Alignment x -> BAM_V1_6_BAM_Alignment

Show BAM_V1_6_BAM_Alignment

Defined in Data.BAM.Version1_6.BAM.Alignment.Base

Methods

showsPrec :: Int -> BAM_V1_6_BAM_Alignment -> ShowS

show :: BAM_V1_6_BAM_Alignment -> String

showList :: [BAM_V1_6_BAM_Alignment] -> ShowS

Eq BAM_V1_6_BAM_Alignment

Defined in Data.BAM.Version1_6.BAM.Alignment.Base

Methods

(==) :: BAM_V1_6_BAM_Alignment -> BAM_V1_6_BAM_Alignment -> Bool

(/=) :: BAM_V1_6_BAM_Alignment -> BAM_V1_6_BAM_Alignment -> Bool

type Rep BAM_V1_6_BAM_Alignment

Defined in Data.BAM.Version1_6.BAM.Alignment.Base

type Rep BAM_V1_6_BAM_Alignment = D1 ('MetaData "BAM_V1_6_BAM_Alignment" "Data.BAM.Version1_6.BAM.Alignment.Base" "hs-samtools-0.10.0.2-inplace" 'False) (C1 ('MetaCons "BAM_V1_6_BAM_Alignment" 'PrefixI 'True) ((((S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_block_size") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Word32) :*: S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_refID") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int32)) :*: (S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_pos") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int32) :*: S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_l_read_name") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Word8))) :*: ((S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_mapq") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Word8) :*: S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_bin") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Word16)) :*: (S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_n_cigar_op") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Word16) :*: S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_flag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Word16)))) :*: (((S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_l_seq") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Word32) :*: S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_next_refID") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int32)) :*: (S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_next_pos") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int32) :*: S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_tlen") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 Int32))) :*: ((S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_read_name") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 ByteString) :*: S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_cigar") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Seq Word32))) :*: (S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_seq") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Seq Word8)) :*: (S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_qual") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 ByteString) :*: S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_optionalfields") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Seq BAM_V1_6_BAM_Alignment_OptionalFields))))))))