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.PG

Contents

SAM version 1.6 program data type
SAM version 1.6 program 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_Program = SAM_V1_6_Program {
}
data SAM_V1_6_Program_Record_Identifier = SAM_V1_6_Program_Record_Identifier {
- sam_v1_6_program_record_identifier_tag :: Seq Word8
- sam_v1_6_program_record_identifier_value :: ByteString
}
data SAM_V1_6_Program_Name = SAM_V1_6_Program_Name {
- sam_v1_6_program_name_tag :: Seq Word8
- sam_v1_6_program_name_value :: ByteString
}
data SAM_V1_6_Program_Command_Line = SAM_V1_6_Program_Command_Line {
- sam_v1_6_program_command_line_tag :: Seq Word8
- sam_v1_6_program_command_line_value :: ByteString
}
data SAM_V1_6_Program_Previous_PG_ID = SAM_V1_6_Program_Previous_PG_ID {
- sam_v1_6_program_previous_pg_id_tag :: Seq Word8
- sam_v1_6_program_previous_pg_id_value :: ByteString
}
data SAM_V1_6_Program_Description = SAM_V1_6_Program_Description {
- sam_v1_6_program_description_tag :: Seq Word8
- sam_v1_6_program_description_value :: ByteString
}
data SAM_V1_6_Program_Version = SAM_V1_6_Program_Version {
- sam_v1_6_program_version_tag :: Seq Word8
- sam_v1_6_program_version_value :: ByteString
}

SAM version 1.6 program data type

data SAM_V1_6_Program Source #

Custom SAM (version 1.6) SAM_V1_6_Program data type. See section 1.3 of the SAM v1.6 specification documentation.

Constructors

SAM_V1_6_Program

Fields

Instances

Instances details

Generic SAM_V1_6_Program Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Associated Types type Rep SAM_V1_6_Program :: Type -> Type # Methods from :: SAM_V1_6_Program -> Rep SAM_V1_6_Program x # to :: Rep SAM_V1_6_Program x -> SAM_V1_6_Program #
Show SAM_V1_6_Program Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Methods showsPrec :: Int -> SAM_V1_6_Program -> ShowS # show :: SAM_V1_6_Program -> String # showList :: [SAM_V1_6_Program] -> ShowS #
type Rep SAM_V1_6_Program Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG type Rep SAM_V1_6_Program = D1 ('MetaData "SAM_V1_6_Program" "Data.SAM.Version1_6.Header.PG" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Program" 'PrefixI 'True) ((S1 ('MetaSel ('Just "sam_v1_6_program_record_identifier") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 SAM_V1_6_Program_Record_Identifier) :: (S1 ('MetaSel ('Just "sam_v1_6_program_name") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Program_Name)) :: S1 ('MetaSel ('Just "sam_v1_6_program_command_line") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Program_Command_Line)))) :: (S1 ('MetaSel ('Just "sam_v1_6_program_previous_pg_id") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Program_Previous_PG_ID)) :: (S1 ('MetaSel ('Just "sam_v1_6_program_description") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Program_Description)) :*: S1 ('MetaSel ('Just "sam_v1_6_program_version") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Program_Version))))))

SAM version 1.6 program data types

data SAM_V1_6_Program_Record_Identifier Source #

ID tag for SAM_V1_6_Program.

Constructors

SAM_V1_6_Program_Record_Identifier
Fields sam_v1_6_program_record_identifier_tag :: Seq Word8 sam_v1_6_program_record_identifier_value :: ByteString

Instances

Instances details

Generic SAM_V1_6_Program_Record_Identifier Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Associated Types type Rep SAM_V1_6_Program_Record_Identifier :: Type -> Type # Methods from :: SAM_V1_6_Program_Record_Identifier -> Rep SAM_V1_6_Program_Record_Identifier x # to :: Rep SAM_V1_6_Program_Record_Identifier x -> SAM_V1_6_Program_Record_Identifier #
Show SAM_V1_6_Program_Record_Identifier Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Methods showsPrec :: Int -> SAM_V1_6_Program_Record_Identifier -> ShowS # show :: SAM_V1_6_Program_Record_Identifier -> String # showList :: [SAM_V1_6_Program_Record_Identifier] -> ShowS #
Eq SAM_V1_6_Program_Record_Identifier Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Methods (==) :: SAM_V1_6_Program_Record_Identifier -> SAM_V1_6_Program_Record_Identifier -> Bool # (/=) :: SAM_V1_6_Program_Record_Identifier -> SAM_V1_6_Program_Record_Identifier -> Bool #
type Rep SAM_V1_6_Program_Record_Identifier Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG type Rep SAM_V1_6_Program_Record_Identifier = D1 ('MetaData "SAM_V1_6_Program_Record_Identifier" "Data.SAM.Version1_6.Header.PG" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Program_Record_Identifier" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_program_record_identifier_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_program_record_identifier_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

data SAM_V1_6_Program_Name Source #

PN tag for SAM_V1_6_Program.

Constructors

SAM_V1_6_Program_Name
Fields sam_v1_6_program_name_tag :: Seq Word8 sam_v1_6_program_name_value :: ByteString

Instances

Instances details

Generic SAM_V1_6_Program_Name Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Associated Types type Rep SAM_V1_6_Program_Name :: Type -> Type # Methods from :: SAM_V1_6_Program_Name -> Rep SAM_V1_6_Program_Name x # to :: Rep SAM_V1_6_Program_Name x -> SAM_V1_6_Program_Name #
Show SAM_V1_6_Program_Name Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Methods showsPrec :: Int -> SAM_V1_6_Program_Name -> ShowS # show :: SAM_V1_6_Program_Name -> String # showList :: [SAM_V1_6_Program_Name] -> ShowS #
Eq SAM_V1_6_Program_Name Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Methods (==) :: SAM_V1_6_Program_Name -> SAM_V1_6_Program_Name -> Bool # (/=) :: SAM_V1_6_Program_Name -> SAM_V1_6_Program_Name -> Bool #
type Rep SAM_V1_6_Program_Name Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG type Rep SAM_V1_6_Program_Name = D1 ('MetaData "SAM_V1_6_Program_Name" "Data.SAM.Version1_6.Header.PG" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Program_Name" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_program_name_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_program_name_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

data SAM_V1_6_Program_Command_Line Source #

CL tag for SAM_V1_6_Program.

Constructors

SAM_V1_6_Program_Command_Line
Fields sam_v1_6_program_command_line_tag :: Seq Word8 sam_v1_6_program_command_line_value :: ByteString

Instances

Instances details

Generic SAM_V1_6_Program_Command_Line Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Associated Types type Rep SAM_V1_6_Program_Command_Line :: Type -> Type # Methods from :: SAM_V1_6_Program_Command_Line -> Rep SAM_V1_6_Program_Command_Line x # to :: Rep SAM_V1_6_Program_Command_Line x -> SAM_V1_6_Program_Command_Line #
Show SAM_V1_6_Program_Command_Line Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Methods showsPrec :: Int -> SAM_V1_6_Program_Command_Line -> ShowS # show :: SAM_V1_6_Program_Command_Line -> String # showList :: [SAM_V1_6_Program_Command_Line] -> ShowS #
Eq SAM_V1_6_Program_Command_Line Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Methods (==) :: SAM_V1_6_Program_Command_Line -> SAM_V1_6_Program_Command_Line -> Bool # (/=) :: SAM_V1_6_Program_Command_Line -> SAM_V1_6_Program_Command_Line -> Bool #
type Rep SAM_V1_6_Program_Command_Line Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG type Rep SAM_V1_6_Program_Command_Line = D1 ('MetaData "SAM_V1_6_Program_Command_Line" "Data.SAM.Version1_6.Header.PG" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Program_Command_Line" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_program_command_line_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_program_command_line_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

data SAM_V1_6_Program_Previous_PG_ID Source #

PP tag for SAM_V1_6_Program.

Constructors

SAM_V1_6_Program_Previous_PG_ID
Fields sam_v1_6_program_previous_pg_id_tag :: Seq Word8 sam_v1_6_program_previous_pg_id_value :: ByteString

Instances

Instances details

Generic SAM_V1_6_Program_Previous_PG_ID Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Associated Types type Rep SAM_V1_6_Program_Previous_PG_ID :: Type -> Type # Methods from :: SAM_V1_6_Program_Previous_PG_ID -> Rep SAM_V1_6_Program_Previous_PG_ID x # to :: Rep SAM_V1_6_Program_Previous_PG_ID x -> SAM_V1_6_Program_Previous_PG_ID #
Show SAM_V1_6_Program_Previous_PG_ID Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Methods showsPrec :: Int -> SAM_V1_6_Program_Previous_PG_ID -> ShowS # show :: SAM_V1_6_Program_Previous_PG_ID -> String # showList :: [SAM_V1_6_Program_Previous_PG_ID] -> ShowS #
Eq SAM_V1_6_Program_Previous_PG_ID Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Methods (==) :: SAM_V1_6_Program_Previous_PG_ID -> SAM_V1_6_Program_Previous_PG_ID -> Bool # (/=) :: SAM_V1_6_Program_Previous_PG_ID -> SAM_V1_6_Program_Previous_PG_ID -> Bool #
type Rep SAM_V1_6_Program_Previous_PG_ID Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG type Rep SAM_V1_6_Program_Previous_PG_ID = D1 ('MetaData "SAM_V1_6_Program_Previous_PG_ID" "Data.SAM.Version1_6.Header.PG" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Program_Previous_PG_ID" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_program_previous_pg_id_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_program_previous_pg_id_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

data SAM_V1_6_Program_Description Source #

DS tag for SAM_V1_6_Program.

Constructors

SAM_V1_6_Program_Description
Fields sam_v1_6_program_description_tag :: Seq Word8 sam_v1_6_program_description_value :: ByteString

Instances

Instances details

Generic SAM_V1_6_Program_Description Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Associated Types type Rep SAM_V1_6_Program_Description :: Type -> Type # Methods from :: SAM_V1_6_Program_Description -> Rep SAM_V1_6_Program_Description x # to :: Rep SAM_V1_6_Program_Description x -> SAM_V1_6_Program_Description #
Show SAM_V1_6_Program_Description Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Methods showsPrec :: Int -> SAM_V1_6_Program_Description -> ShowS # show :: SAM_V1_6_Program_Description -> String # showList :: [SAM_V1_6_Program_Description] -> ShowS #
Eq SAM_V1_6_Program_Description Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Methods (==) :: SAM_V1_6_Program_Description -> SAM_V1_6_Program_Description -> Bool # (/=) :: SAM_V1_6_Program_Description -> SAM_V1_6_Program_Description -> Bool #
type Rep SAM_V1_6_Program_Description Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG type Rep SAM_V1_6_Program_Description = D1 ('MetaData "SAM_V1_6_Program_Description" "Data.SAM.Version1_6.Header.PG" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Program_Description" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_program_description_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_program_description_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

data SAM_V1_6_Program_Version Source #

VN tag for SAM_V1_6_Program.

Constructors

SAM_V1_6_Program_Version
Fields sam_v1_6_program_version_tag :: Seq Word8 sam_v1_6_program_version_value :: ByteString

Instances

Instances details

Generic SAM_V1_6_Program_Version Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Associated Types type Rep SAM_V1_6_Program_Version :: Type -> Type # Methods from :: SAM_V1_6_Program_Version -> Rep SAM_V1_6_Program_Version x # to :: Rep SAM_V1_6_Program_Version x -> SAM_V1_6_Program_Version #
Show SAM_V1_6_Program_Version Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Methods showsPrec :: Int -> SAM_V1_6_Program_Version -> ShowS # show :: SAM_V1_6_Program_Version -> String # showList :: [SAM_V1_6_Program_Version] -> ShowS #
Eq SAM_V1_6_Program_Version Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG Methods (==) :: SAM_V1_6_Program_Version -> SAM_V1_6_Program_Version -> Bool # (/=) :: SAM_V1_6_Program_Version -> SAM_V1_6_Program_Version -> Bool #
type Rep SAM_V1_6_Program_Version Source #
Instance details Defined in Data.SAM.Version1_6.Header.PG type Rep SAM_V1_6_Program_Version = D1 ('MetaData "SAM_V1_6_Program_Version" "Data.SAM.Version1_6.Header.PG" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Program_Version" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_program_version_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_program_version_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))