Data.SAM.Version1_6.Base

WARNING

This module is considered internal.

The Package Versioning Policy does not apply.

The contents of this module may change in any way whatsoever and without any warning between minor versions of this package.

Authors importing this library are expected to track development closely.

All credit goes to the author(s)/maintainer(s) of the containers library for the above warning text.

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 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

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

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-0.4.0.0-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 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))))))