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

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.

Synopsis

data SAM_V1_6_File_Level_Metadata = SAM_V1_6_File_Level_Metadata {
}
data SAM_V1_6_File_Level_Metadata_Format_Version = SAM_V1_6_File_Level_Metadata_Format_Version {
- sam_v1_6_file_level_metadata_format_version_tag :: Seq Word8
- sam_v1_6_file_level_metadata_format_version_value :: ByteString
}
data SAM_V1_6_File_Level_Metadata_Sorting_Order = SAM_V1_6_File_Level_Metadata_Sorting_Order {
- sam_v1_6_file_level_metadata_sorting_order_tag :: Seq Word8
- sam_v1_6_file_level_metadata_sorting_order_value :: ByteString
}
data SAM_V1_6_File_Level_Metadata_Alignment_Grouping = SAM_V1_6_File_Level_Metadata_Alignment_Grouping {
- sam_v1_6_file_level_metadata_alignment_grouping_tag :: Seq Word8
- sam_v1_6_file_level_metadata_alignment_grouping_value :: ByteString
}
data SAM_V1_6_File_Level_Metadata_SubSorting_Order = SAM_V1_6_File_Level_Metadata_SubSorting_Order {
- sam_v1_6_file_level_metadata_subsorting_order_tag :: Seq Word8
- 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 #
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-0.2.0.0-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

data 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_tag :: Seq Word8 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 #	Show instance for `SAM_V1_6_File_Level_Metadata_Format_Version`.
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 #	Eq instance for `SAM_V1_6_File_Level_Metadata_Format_Version`.
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-0.2.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_File_Level_Metadata_Format_Version" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_format_version_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_format_version_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

data 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_tag :: Seq Word8 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 #	Show instance for `SAM_V1_6_File_Level_Metadata_Sorting_Order`.
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 #	Eq instance for `SAM_V1_6_File_Level_Metadata_Sorting_Order`.
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-0.2.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_File_Level_Metadata_Sorting_Order" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_sorting_order_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_sorting_order_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

data 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_tag :: Seq Word8 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 #	Show instance for `SAM_V1_6_File_Level_Metadata_Alignment_Grouping`.
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 #	Eq instance for `SAM_V1_6_File_Level_Metadata_Alignment_Grouping`.
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-0.2.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_File_Level_Metadata_Alignment_Grouping" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_alignment_grouping_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_alignment_grouping_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

data 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_tag :: Seq Word8 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 #	Show instance for `SAM_V1_6_File_Level_Metadata_SubSorting_Order`.
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 #	Eq instance for `SAM_V1_6_File_Level_Metadata_SubSorting_Order`.
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-0.2.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_File_Level_Metadata_SubSorting_Order" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_subsorting_order_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_subsorting_order_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))