Copyright	(c) Matthew Mosior 2024
License	BSD-style
Maintainer	mattm.github@gmail.com
Portability	portable
Safe Haskell	Safe-Inferred
Language	Haskell2010

Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base

Contents

BAM version 1.6 alignment optional fields data type

Description

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

Synopsis

data BAM_V1_6_BAM_Alignment_OptionalFields = BAM_V1_6_BAM_Alignment_OptionalFields {
}
data BAM_V1_6_BAM_Alignment_OptionalFields_SumType
- = AOPT
- | SmallCOPT
- | BigCOPT
- | SmallIOPT
- | BigIOPT
- | SmallSOPT
- | BigSOPT
- | FOPT
- | ZOPT
- | HOPT
- | BOPT
- | Empty

BAM version 1.6 alignment optional fields data type

data BAM_V1_6_BAM_Alignment_OptionalFields Source #

Custom BAM (version 1.6) BAM_V1_6_BAM_Alignment_Optional_Fields data type.

See section 4.2 of the SAM v1.6 specification documentation.

Constructors

BAM_V1_6_BAM_Alignment_OptionalFields

Fields

bam_v1_6_bam_alignment_optionalfields_aopt :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_AOPT
A - [!-~] - Printable character.
bam_v1_6_bam_alignment_optionalfields_smallcopt :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT
c - [0-9]+ - Int8 (signed).
bam_v1_6_bam_alignment_optionalfields_bigcopt :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT
C - [0-9]+ - Word8 (unsigned).
bam_v1_6_bam_alignment_optionalfields_smalliopt :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT
i - [0-9]+ - Int32 (signed).
bam_v1_6_bam_alignment_optionalfields_bigiopt :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT
I - [0-9]+ - Word32 (unsigned).
bam_v1_6_bam_alignment_optionalfields_smallsopt :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT
s - [0-9]+ - Int16 (signed).
bam_v1_6_bam_alignment_optionalfields_bigsopt :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT
S - [0-9]+ - Word16 (unsigned).
bam_v1_6_bam_alignment_optionalfields_fopt :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_FOPT
f - [-+]?[0-9]*.?[0-9]+([eE][-+]?[0-9]+)? - Single-precision floating number.
bam_v1_6_bam_alignment_optionalfields_zopt :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT
Z - [ !-~]* - Printable string, including space.
bam_v1_6_bam_alignment_optionalfields_hopt :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_HOPT
H - ([0-9A-F][0-9A-F])* - Byte array in the Hex format.
bam_v1_6_bam_alignment_optionalfields_bopt :: Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT
B - [cCsSiIf](,[-+]?[0-9]*.?[0-9]+([eE][-+]?[0-9]+)?)* - Integer or numeric array.

Instances

Instances details

Generic BAM_V1_6_BAM_Alignment_OptionalFields Source #
Instance details Defined in Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base Associated Types type Rep BAM_V1_6_BAM_Alignment_OptionalFields :: Type -> Type # Methods from :: BAM_V1_6_BAM_Alignment_OptionalFields -> Rep BAM_V1_6_BAM_Alignment_OptionalFields x # to :: Rep BAM_V1_6_BAM_Alignment_OptionalFields x -> BAM_V1_6_BAM_Alignment_OptionalFields #
Show BAM_V1_6_BAM_Alignment_OptionalFields Source #
Instance details Defined in Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base Methods showsPrec :: Int -> BAM_V1_6_BAM_Alignment_OptionalFields -> ShowS # show :: BAM_V1_6_BAM_Alignment_OptionalFields -> String # showList :: [BAM_V1_6_BAM_Alignment_OptionalFields] -> ShowS #
Eq BAM_V1_6_BAM_Alignment_OptionalFields Source #
Instance details Defined in Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base Methods (==) :: BAM_V1_6_BAM_Alignment_OptionalFields -> BAM_V1_6_BAM_Alignment_OptionalFields -> Bool # (/=) :: BAM_V1_6_BAM_Alignment_OptionalFields -> BAM_V1_6_BAM_Alignment_OptionalFields -> Bool #
type Rep BAM_V1_6_BAM_Alignment_OptionalFields Source #
Instance details Defined in Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base type Rep BAM_V1_6_BAM_Alignment_OptionalFields = D1 ('MetaData "BAM_V1_6_BAM_Alignment_OptionalFields" "Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base" "hs-samtools-0.10.0.2-inplace" 'False) (C1 ('MetaCons "BAM_V1_6_BAM_Alignment_OptionalFields" 'PrefixI 'True) (((S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_optionalfields_aopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe BAM_V1_6_BAM_Alignment_OptionalFields_AOPT)) :: S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_optionalfields_smallcopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe BAM_V1_6_BAM_Alignment_OptionalFields_SmallCOPT))) :: (S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_optionalfields_bigcopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BigCOPT)) :: (S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_optionalfields_smalliopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe BAM_V1_6_BAM_Alignment_OptionalFields_SmallIOPT)) :: S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_optionalfields_bigiopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BigIOPT))))) :: ((S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_optionalfields_smallsopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe BAM_V1_6_BAM_Alignment_OptionalFields_SmallSOPT)) :: (S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_optionalfields_bigsopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BigSOPT)) :: S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_optionalfields_fopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe BAM_V1_6_BAM_Alignment_OptionalFields_FOPT)))) :: (S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_optionalfields_zopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe BAM_V1_6_BAM_Alignment_OptionalFields_ZOPT)) :: (S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_optionalfields_hopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe BAM_V1_6_BAM_Alignment_OptionalFields_HOPT)) :: S1 ('MetaSel ('Just "bam_v1_6_bam_alignment_optionalfields_bopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedStrict) (Rec0 (Maybe BAM_V1_6_BAM_Alignment_OptionalFields_BOPT)))))))

data BAM_V1_6_BAM_Alignment_OptionalFields_SumType Source #

Sum type that can represent any of the BAM_V1_6_BAM_Alignment_OptionalFields types.

Constructors

AOPT
SmallCOPT
BigCOPT
SmallIOPT
BigIOPT
SmallSOPT
BigSOPT
FOPT
ZOPT
HOPT
BOPT
Empty

Instances

Instances details

Generic BAM_V1_6_BAM_Alignment_OptionalFields_SumType Source #
Instance details Defined in Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base Associated Types type Rep BAM_V1_6_BAM_Alignment_OptionalFields_SumType :: Type -> Type # Methods from :: BAM_V1_6_BAM_Alignment_OptionalFields_SumType -> Rep BAM_V1_6_BAM_Alignment_OptionalFields_SumType x # to :: Rep BAM_V1_6_BAM_Alignment_OptionalFields_SumType x -> BAM_V1_6_BAM_Alignment_OptionalFields_SumType #
Eq BAM_V1_6_BAM_Alignment_OptionalFields_SumType Source #
Instance details Defined in Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base Methods (==) :: BAM_V1_6_BAM_Alignment_OptionalFields_SumType -> BAM_V1_6_BAM_Alignment_OptionalFields_SumType -> Bool # (/=) :: BAM_V1_6_BAM_Alignment_OptionalFields_SumType -> BAM_V1_6_BAM_Alignment_OptionalFields_SumType -> Bool #
type Rep BAM_V1_6_BAM_Alignment_OptionalFields_SumType Source #
Instance details Defined in Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base type Rep BAM_V1_6_BAM_Alignment_OptionalFields_SumType = D1 ('MetaData "BAM_V1_6_BAM_Alignment_OptionalFields_SumType" "Data.BAM.Version1_6.BAM.Alignment.OptionalFields.Base" "hs-samtools-0.10.0.2-inplace" 'False) (((C1 ('MetaCons "AOPT" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "SmallCOPT" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "BigCOPT" 'PrefixI 'False) (U1 :: Type -> Type))) :+: (C1 ('MetaCons "SmallIOPT" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "BigIOPT" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "SmallSOPT" 'PrefixI 'False) (U1 :: Type -> Type)))) :+: ((C1 ('MetaCons "BigSOPT" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "FOPT" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "ZOPT" 'PrefixI 'False) (U1 :: Type -> Type))) :+: (C1 ('MetaCons "HOPT" 'PrefixI 'False) (U1 :: Type -> Type) :+: (C1 ('MetaCons "BOPT" 'PrefixI 'False) (U1 :: Type -> Type) :+: C1 ('MetaCons "Empty" 'PrefixI 'False) (U1 :: Type -> Type)))))