hs-samtools-0.2.0.0: Read and write SAM, BAM, and CRAM files.
Copyright(c) Matthew Mosior 2023
LicenseBSD-style
Maintainermattm.github@gmail.com
Portabilityportable
Safe HaskellSafe-Inferred
LanguageHaskell2010

Data.SAM.Version1_6.Header.PG

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

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 #

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-0.2.0.0-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

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 #

Show instance for SAM_V1_6_Program_Record_Identifier.

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 #

Eq instance for SAM_V1_6_Program_Record_Identifier.

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-0.2.0.0-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

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 #

Show instance for SAM_V1_6_Program_Name.

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 #

Eq instance for SAM_V1_6_Program_Name.

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-0.2.0.0-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

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 #

Show instance for SAM_V1_6_Program_Command_Line.

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 #

Eq instance for SAM_V1_6_Program_Command_Line.

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-0.2.0.0-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

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 #

Show instance for SAM_V1_6_Program_Previous_PG_ID.

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 #

Eq instance for SAM_V1_6_Program_Previous_PG_ID.

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-0.2.0.0-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

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 #

Show instance for SAM_V1_6_Program_Description.

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 #

Eq instance for SAM_V1_6_Program_Description.

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-0.2.0.0-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

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 #

Show instance for SAM_V1_6_Program_Version.

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 #

Eq instance for SAM_V1_6_Program_Version.

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-0.2.0.0-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)))