Copyright	(c) Matthew Mosior 2023
License	BSD-style
Maintainer	mattm.github@gmail.com
Portability	portable
Safe Haskell	Safe-Inferred
Language	Haskell2010

Data.SAM.Version1_6.Header.HD

Contents

SAM version 1.6 File-level metadata data type
SAM version 1.6 File-Level Metadata data types

Description

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

Synopsis

data SAM_V1_6_File_Level_Metadata = SAM_V1_6_File_Level_Metadata {
}
newtype SAM_V1_6_File_Level_Metadata_Format_Version = SAM_V1_6_File_Level_Metadata_Format_Version {
- sam_v1_6_file_level_metadata_format_version_value :: ByteString
}
newtype SAM_V1_6_File_Level_Metadata_Sorting_Order = SAM_V1_6_File_Level_Metadata_Sorting_Order {
- sam_v1_6_file_level_metadata_sorting_order_value :: ByteString
}
newtype SAM_V1_6_File_Level_Metadata_Alignment_Grouping = SAM_V1_6_File_Level_Metadata_Alignment_Grouping {
- sam_v1_6_file_level_metadata_alignment_grouping_value :: ByteString
}
newtype SAM_V1_6_File_Level_Metadata_SubSorting_Order = SAM_V1_6_File_Level_Metadata_SubSorting_Order {
- sam_v1_6_file_level_metadata_subsorting_order_value :: ByteString
}

SAM version 1.6 File-level metadata data type

data SAM_V1_6_File_Level_Metadata Source #

Custom SAM (version 1.6) SAM_V1_6_File_Level_Metadata data type.

See section 1.3 of the SAM v1.6 specification documentation.

Constructors

SAM_V1_6_File_Level_Metadata

Fields

Instances

Instances details

Generic SAM_V1_6_File_Level_Metadata Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Associated Types type Rep SAM_V1_6_File_Level_Metadata :: Type -> Type # Methods from :: SAM_V1_6_File_Level_Metadata -> Rep SAM_V1_6_File_Level_Metadata x # to :: Rep SAM_V1_6_File_Level_Metadata x -> SAM_V1_6_File_Level_Metadata #
Show SAM_V1_6_File_Level_Metadata Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Methods showsPrec :: Int -> SAM_V1_6_File_Level_Metadata -> ShowS # show :: SAM_V1_6_File_Level_Metadata -> String # showList :: [SAM_V1_6_File_Level_Metadata] -> ShowS #
Eq SAM_V1_6_File_Level_Metadata Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Methods (==) :: SAM_V1_6_File_Level_Metadata -> SAM_V1_6_File_Level_Metadata -> Bool # (/=) :: SAM_V1_6_File_Level_Metadata -> SAM_V1_6_File_Level_Metadata -> Bool #
type Rep SAM_V1_6_File_Level_Metadata Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD type Rep SAM_V1_6_File_Level_Metadata = D1 ('MetaData "SAM_V1_6_File_Level_Metadata" "Data.SAM.Version1_6.Header.HD" "hs-samtools-0.9.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_File_Level_Metadata" 'PrefixI 'True) ((S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_format_version") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 SAM_V1_6_File_Level_Metadata_Format_Version) :: S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_sorting_order") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order))) :: (S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_alignment_grouping") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping)) :*: S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_subsorting_order") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order)))))

SAM version 1.6 File-Level Metadata data types

newtype SAM_V1_6_File_Level_Metadata_Format_Version Source #

VN tag for SAM_V1_6_File_Level_Metadata.

Constructors

SAM_V1_6_File_Level_Metadata_Format_Version
Fields sam_v1_6_file_level_metadata_format_version_value :: ByteString

Instances

Instances details

Generic SAM_V1_6_File_Level_Metadata_Format_Version Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Associated Types type Rep SAM_V1_6_File_Level_Metadata_Format_Version :: Type -> Type # Methods from :: SAM_V1_6_File_Level_Metadata_Format_Version -> Rep SAM_V1_6_File_Level_Metadata_Format_Version x # to :: Rep SAM_V1_6_File_Level_Metadata_Format_Version x -> SAM_V1_6_File_Level_Metadata_Format_Version #
Show SAM_V1_6_File_Level_Metadata_Format_Version Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Methods showsPrec :: Int -> SAM_V1_6_File_Level_Metadata_Format_Version -> ShowS # show :: SAM_V1_6_File_Level_Metadata_Format_Version -> String # showList :: [SAM_V1_6_File_Level_Metadata_Format_Version] -> ShowS #
Eq SAM_V1_6_File_Level_Metadata_Format_Version Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Methods (==) :: SAM_V1_6_File_Level_Metadata_Format_Version -> SAM_V1_6_File_Level_Metadata_Format_Version -> Bool # (/=) :: SAM_V1_6_File_Level_Metadata_Format_Version -> SAM_V1_6_File_Level_Metadata_Format_Version -> Bool #
type Rep SAM_V1_6_File_Level_Metadata_Format_Version Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD type Rep SAM_V1_6_File_Level_Metadata_Format_Version = D1 ('MetaData "SAM_V1_6_File_Level_Metadata_Format_Version" "Data.SAM.Version1_6.Header.HD" "hs-samtools-0.9.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_File_Level_Metadata_Format_Version" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_format_version_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

newtype SAM_V1_6_File_Level_Metadata_Sorting_Order Source #

SO tag for SAM_V1_6_File_Level_Metadata.

Constructors

SAM_V1_6_File_Level_Metadata_Sorting_Order
Fields sam_v1_6_file_level_metadata_sorting_order_value :: ByteString

Instances

Instances details

Generic SAM_V1_6_File_Level_Metadata_Sorting_Order Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Associated Types type Rep SAM_V1_6_File_Level_Metadata_Sorting_Order :: Type -> Type # Methods from :: SAM_V1_6_File_Level_Metadata_Sorting_Order -> Rep SAM_V1_6_File_Level_Metadata_Sorting_Order x # to :: Rep SAM_V1_6_File_Level_Metadata_Sorting_Order x -> SAM_V1_6_File_Level_Metadata_Sorting_Order #
Show SAM_V1_6_File_Level_Metadata_Sorting_Order Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Methods showsPrec :: Int -> SAM_V1_6_File_Level_Metadata_Sorting_Order -> ShowS # show :: SAM_V1_6_File_Level_Metadata_Sorting_Order -> String # showList :: [SAM_V1_6_File_Level_Metadata_Sorting_Order] -> ShowS #
Eq SAM_V1_6_File_Level_Metadata_Sorting_Order Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Methods (==) :: SAM_V1_6_File_Level_Metadata_Sorting_Order -> SAM_V1_6_File_Level_Metadata_Sorting_Order -> Bool # (/=) :: SAM_V1_6_File_Level_Metadata_Sorting_Order -> SAM_V1_6_File_Level_Metadata_Sorting_Order -> Bool #
type Rep SAM_V1_6_File_Level_Metadata_Sorting_Order Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD type Rep SAM_V1_6_File_Level_Metadata_Sorting_Order = D1 ('MetaData "SAM_V1_6_File_Level_Metadata_Sorting_Order" "Data.SAM.Version1_6.Header.HD" "hs-samtools-0.9.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_File_Level_Metadata_Sorting_Order" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_sorting_order_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

newtype SAM_V1_6_File_Level_Metadata_Alignment_Grouping Source #

GO tag for SAM_V1_6_File_Level_Metadata.

Constructors

SAM_V1_6_File_Level_Metadata_Alignment_Grouping
Fields sam_v1_6_file_level_metadata_alignment_grouping_value :: ByteString

Instances

Instances details

Generic SAM_V1_6_File_Level_Metadata_Alignment_Grouping Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Associated Types type Rep SAM_V1_6_File_Level_Metadata_Alignment_Grouping :: Type -> Type # Methods from :: SAM_V1_6_File_Level_Metadata_Alignment_Grouping -> Rep SAM_V1_6_File_Level_Metadata_Alignment_Grouping x # to :: Rep SAM_V1_6_File_Level_Metadata_Alignment_Grouping x -> SAM_V1_6_File_Level_Metadata_Alignment_Grouping #
Show SAM_V1_6_File_Level_Metadata_Alignment_Grouping Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Methods showsPrec :: Int -> SAM_V1_6_File_Level_Metadata_Alignment_Grouping -> ShowS # show :: SAM_V1_6_File_Level_Metadata_Alignment_Grouping -> String # showList :: [SAM_V1_6_File_Level_Metadata_Alignment_Grouping] -> ShowS #
Eq SAM_V1_6_File_Level_Metadata_Alignment_Grouping Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Methods (==) :: SAM_V1_6_File_Level_Metadata_Alignment_Grouping -> SAM_V1_6_File_Level_Metadata_Alignment_Grouping -> Bool # (/=) :: SAM_V1_6_File_Level_Metadata_Alignment_Grouping -> SAM_V1_6_File_Level_Metadata_Alignment_Grouping -> Bool #
type Rep SAM_V1_6_File_Level_Metadata_Alignment_Grouping Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD type Rep SAM_V1_6_File_Level_Metadata_Alignment_Grouping = D1 ('MetaData "SAM_V1_6_File_Level_Metadata_Alignment_Grouping" "Data.SAM.Version1_6.Header.HD" "hs-samtools-0.9.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_File_Level_Metadata_Alignment_Grouping" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_alignment_grouping_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

newtype SAM_V1_6_File_Level_Metadata_SubSorting_Order Source #

SS tag for SAM_V1_6_File_Level_Metadata.

Constructors

SAM_V1_6_File_Level_Metadata_SubSorting_Order
Fields sam_v1_6_file_level_metadata_subsorting_order_value :: ByteString

Instances

Instances details

Generic SAM_V1_6_File_Level_Metadata_SubSorting_Order Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Associated Types type Rep SAM_V1_6_File_Level_Metadata_SubSorting_Order :: Type -> Type # Methods from :: SAM_V1_6_File_Level_Metadata_SubSorting_Order -> Rep SAM_V1_6_File_Level_Metadata_SubSorting_Order x # to :: Rep SAM_V1_6_File_Level_Metadata_SubSorting_Order x -> SAM_V1_6_File_Level_Metadata_SubSorting_Order #
Show SAM_V1_6_File_Level_Metadata_SubSorting_Order Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Methods showsPrec :: Int -> SAM_V1_6_File_Level_Metadata_SubSorting_Order -> ShowS # show :: SAM_V1_6_File_Level_Metadata_SubSorting_Order -> String # showList :: [SAM_V1_6_File_Level_Metadata_SubSorting_Order] -> ShowS #
Eq SAM_V1_6_File_Level_Metadata_SubSorting_Order Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD Methods (==) :: SAM_V1_6_File_Level_Metadata_SubSorting_Order -> SAM_V1_6_File_Level_Metadata_SubSorting_Order -> Bool # (/=) :: SAM_V1_6_File_Level_Metadata_SubSorting_Order -> SAM_V1_6_File_Level_Metadata_SubSorting_Order -> Bool #
type Rep SAM_V1_6_File_Level_Metadata_SubSorting_Order Source #
Instance details Defined in Data.SAM.Version1_6.Header.HD type Rep SAM_V1_6_File_Level_Metadata_SubSorting_Order = D1 ('MetaData "SAM_V1_6_File_Level_Metadata_SubSorting_Order" "Data.SAM.Version1_6.Header.HD" "hs-samtools-0.9.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_File_Level_Metadata_SubSorting_Order" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_subsorting_order_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))