Data.SAM.Version1_6.Base

Description

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

SAM version 1.6 data type

data SAM_V1_6

Custom SAM_V1_6 (SAM version 1.6) data type.

See the SAM v1.6 specification documentation.

Constructors

SAM_V1_6

Fields

• sam_v1_6_file_level_metadata :: Maybe SAM_V1_6_File_Level_Metadata

  File-level metadata. Optional. If present, there must be only one @HD line and it must be the first line of the file.

• sam_v1_6_reference_sequence_dictionary :: Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary)

  Reference sequence dictionary. The order of @SQ lines defines the alignment sorting order.

• sam_v1_6_read_group :: Maybe (Seq SAM_V1_6_Read_Group)

  Read group. Unordered multiple @RG lines are allowed.

• sam_v1_6_program :: Maybe SAM_V1_6_Program

  Program.

• sam_v1_6_one_line_comment :: Maybe (Seq SAM_V1_6_One_Line_Comment)

  One-line text comment. Unordered multiple @CO lines are allowed. UTF-8 encoding may be used.

• sam_v1_6_alignment :: Seq SAM_V1_6_Alignment

  The alignment section (mandatory and optional fields).

Instances

Generic SAM_V1_6

Defined in Data.SAM.Version1_6.Base

Associated Types

type Rep SAM_V1_6 :: Type -> Type

Methods

from :: SAM_V1_6 -> Rep SAM_V1_6 x

to :: Rep SAM_V1_6 x -> SAM_V1_6

Show SAM_V1_6

Defined in Data.SAM.Version1_6.Base

Methods

showsPrec :: Int -> SAM_V1_6 -> ShowS

show :: SAM_V1_6 -> String

showList :: [SAM_V1_6] -> ShowS

Eq SAM_V1_6

Defined in Data.SAM.Version1_6.Base

Methods

(==) :: SAM_V1_6 -> SAM_V1_6 -> Bool

(/=) :: SAM_V1_6 -> SAM_V1_6 -> Bool

type Rep SAM_V1_6

Defined in Data.SAM.Version1_6.Base

type Rep SAM_V1_6 = D1 ('MetaData "SAM_V1_6" "Data.SAM.Version1_6.Base" "hs-samtools-0.9.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6" 'PrefixI 'True) ((S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_File_Level_Metadata)) :*: (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary))) :*: S1 ('MetaSel ('Just "sam_v1_6_read_group") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (Seq SAM_V1_6_Read_Group))))) :*: (S1 ('MetaSel ('Just "sam_v1_6_program") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Program)) :*: (S1 ('MetaSel ('Just "sam_v1_6_one_line_comment") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (Seq SAM_V1_6_One_Line_Comment))) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq SAM_V1_6_Alignment))))))