Data.SAM.Version1_6.Alignment.BOPT

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.

SAM version 1.6 alignment optional fields data type

data SAM_V1_6_Alignment_BOPT

Custom SAM (version 1.6) SAM_V1_6_Alignment_BOPT data type. See section 1.5 of the SAM v1.6 specification documentation.

Constructors

SAM_V1_6_Alignment_BOPT

Fields

• sam_v1_6_alignment_bopt_int8 :: Maybe SAM_V1_6_Alignment_BOPT_Int8
• sam_v1_6_alignment_bopt_word8 :: Maybe SAM_V1_6_Alignment_BOPT_Word8
• sam_v1_6_alignment_bopt_int16 :: Maybe SAM_V1_6_Alignment_BOPT_Int16
• sam_v1_6_alignment_bopt_word16 :: Maybe SAM_V1_6_Alignment_BOPT_Word16
• sam_v1_6_alignment_bopt_int32 :: Maybe SAM_V1_6_Alignment_BOPT_Int32
• sam_v1_6_alignment_bopt_word32 :: Maybe SAM_V1_6_Alignment_BOPT_Word32

Instances

Generic SAM_V1_6_Alignment_BOPT

Defined in Data.SAM.Version1_6.Alignment.BOPT

Associated Types

type Rep SAM_V1_6_Alignment_BOPT :: Type -> Type

Methods

from :: SAM_V1_6_Alignment_BOPT -> Rep SAM_V1_6_Alignment_BOPT x

to :: Rep SAM_V1_6_Alignment_BOPT x -> SAM_V1_6_Alignment_BOPT

Show SAM_V1_6_Alignment_BOPT

Defined in Data.SAM.Version1_6.Alignment.BOPT

Methods

showsPrec :: Int -> SAM_V1_6_Alignment_BOPT -> ShowS

show :: SAM_V1_6_Alignment_BOPT -> String

showList :: [SAM_V1_6_Alignment_BOPT] -> ShowS

type Rep SAM_V1_6_Alignment_BOPT

Defined in Data.SAM.Version1_6.Alignment.BOPT

type Rep SAM_V1_6_Alignment_BOPT = D1 ('MetaData "SAM_V1_6_Alignment_BOPT" "Data.SAM.Version1_6.Alignment.BOPT" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Alignment_BOPT" 'PrefixI 'True) ((S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_int8") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Alignment_BOPT_Int8)) :*: (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_word8") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Alignment_BOPT_Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_int16") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Alignment_BOPT_Int16)))) :*: (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_word16") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Alignment_BOPT_Word16)) :*: (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_int32") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Alignment_BOPT_Int32)) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_word32") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Alignment_BOPT_Word32))))))

data SAM_V1_6_Alignment_BOPT_Int8

cCsSiIf of the last optional field (type B). See section 1.5 of the SAM v1.6 specification documentation.

Constructors

SAM_V1_6_Alignment_BOPT_Int8

Fields

• sam_v1_6_alignment_bopt_int8_tag :: Seq Word8
• sam_v1_6_alignment_bopt_int8_type :: Word8
• sam_v1_6_alignment_bopt_int8_value :: Seq Int8

Instances

Generic SAM_V1_6_Alignment_BOPT_Int8

Defined in Data.SAM.Version1_6.Alignment.BOPT

Associated Types

type Rep SAM_V1_6_Alignment_BOPT_Int8 :: Type -> Type

Methods

from :: SAM_V1_6_Alignment_BOPT_Int8 -> Rep SAM_V1_6_Alignment_BOPT_Int8 x

to :: Rep SAM_V1_6_Alignment_BOPT_Int8 x -> SAM_V1_6_Alignment_BOPT_Int8

Show SAM_V1_6_Alignment_BOPT_Int8

Defined in Data.SAM.Version1_6.Alignment.BOPT

Methods

showsPrec :: Int -> SAM_V1_6_Alignment_BOPT_Int8 -> ShowS

show :: SAM_V1_6_Alignment_BOPT_Int8 -> String

showList :: [SAM_V1_6_Alignment_BOPT_Int8] -> ShowS

Eq SAM_V1_6_Alignment_BOPT_Int8

Defined in Data.SAM.Version1_6.Alignment.BOPT

Methods

(==) :: SAM_V1_6_Alignment_BOPT_Int8 -> SAM_V1_6_Alignment_BOPT_Int8 -> Bool

(/=) :: SAM_V1_6_Alignment_BOPT_Int8 -> SAM_V1_6_Alignment_BOPT_Int8 -> Bool

type Rep SAM_V1_6_Alignment_BOPT_Int8

Defined in Data.SAM.Version1_6.Alignment.BOPT

type Rep SAM_V1_6_Alignment_BOPT_Int8 = D1 ('MetaData "SAM_V1_6_Alignment_BOPT_Int8" "Data.SAM.Version1_6.Alignment.BOPT" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Alignment_BOPT_Int8" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_int8_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_int8_type") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Word8) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_int8_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Int8)))))

data SAM_V1_6_Alignment_BOPT_Word8

cCsSiIf of the last optional field (type B). See section 1.5 of the SAM v1.6 specification documentation.

Constructors

SAM_V1_6_Alignment_BOPT_Word8

Fields

• sam_v1_6_alignment_bopt_word8_tag :: Seq Word8
• sam_v1_6_alignment_bopt_word8_type :: Word8
• sam_v1_6_alignment_bopt_word8_value :: Seq Word8

Instances

Generic SAM_V1_6_Alignment_BOPT_Word8

Defined in Data.SAM.Version1_6.Alignment.BOPT

Associated Types

type Rep SAM_V1_6_Alignment_BOPT_Word8 :: Type -> Type

Methods

from :: SAM_V1_6_Alignment_BOPT_Word8 -> Rep SAM_V1_6_Alignment_BOPT_Word8 x

to :: Rep SAM_V1_6_Alignment_BOPT_Word8 x -> SAM_V1_6_Alignment_BOPT_Word8

Show SAM_V1_6_Alignment_BOPT_Word8

Defined in Data.SAM.Version1_6.Alignment.BOPT

Methods

showsPrec :: Int -> SAM_V1_6_Alignment_BOPT_Word8 -> ShowS

show :: SAM_V1_6_Alignment_BOPT_Word8 -> String

showList :: [SAM_V1_6_Alignment_BOPT_Word8] -> ShowS

Eq SAM_V1_6_Alignment_BOPT_Word8

Defined in Data.SAM.Version1_6.Alignment.BOPT

Methods

(==) :: SAM_V1_6_Alignment_BOPT_Word8 -> SAM_V1_6_Alignment_BOPT_Word8 -> Bool

(/=) :: SAM_V1_6_Alignment_BOPT_Word8 -> SAM_V1_6_Alignment_BOPT_Word8 -> Bool

type Rep SAM_V1_6_Alignment_BOPT_Word8

Defined in Data.SAM.Version1_6.Alignment.BOPT

type Rep SAM_V1_6_Alignment_BOPT_Word8 = D1 ('MetaData "SAM_V1_6_Alignment_BOPT_Word8" "Data.SAM.Version1_6.Alignment.BOPT" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Alignment_BOPT_Word8" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_word8_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_word8_type") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Word8) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_word8_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)))))

data SAM_V1_6_Alignment_BOPT_Int16

cCsSiIf of the last optional field (type B). See section 1.5 of the SAM v1.6 specification documentation.

Constructors

SAM_V1_6_Alignment_BOPT_Int16

Fields

• sam_v1_6_alignment_bopt_int16_tag :: Seq Word8
• sam_v1_6_alignment_bopt_int16_type :: Word8
• sam_v1_6_alignment_bopt_int16_value :: Seq Int16

Instances

Generic SAM_V1_6_Alignment_BOPT_Int16

Defined in Data.SAM.Version1_6.Alignment.BOPT

Associated Types

type Rep SAM_V1_6_Alignment_BOPT_Int16 :: Type -> Type

Methods

from :: SAM_V1_6_Alignment_BOPT_Int16 -> Rep SAM_V1_6_Alignment_BOPT_Int16 x

to :: Rep SAM_V1_6_Alignment_BOPT_Int16 x -> SAM_V1_6_Alignment_BOPT_Int16

Show SAM_V1_6_Alignment_BOPT_Int16

Defined in Data.SAM.Version1_6.Alignment.BOPT

Methods

showsPrec :: Int -> SAM_V1_6_Alignment_BOPT_Int16 -> ShowS

show :: SAM_V1_6_Alignment_BOPT_Int16 -> String

showList :: [SAM_V1_6_Alignment_BOPT_Int16] -> ShowS

Eq SAM_V1_6_Alignment_BOPT_Int16

Defined in Data.SAM.Version1_6.Alignment.BOPT

Methods

(==) :: SAM_V1_6_Alignment_BOPT_Int16 -> SAM_V1_6_Alignment_BOPT_Int16 -> Bool

(/=) :: SAM_V1_6_Alignment_BOPT_Int16 -> SAM_V1_6_Alignment_BOPT_Int16 -> Bool

type Rep SAM_V1_6_Alignment_BOPT_Int16

Defined in Data.SAM.Version1_6.Alignment.BOPT

type Rep SAM_V1_6_Alignment_BOPT_Int16 = D1 ('MetaData "SAM_V1_6_Alignment_BOPT_Int16" "Data.SAM.Version1_6.Alignment.BOPT" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Alignment_BOPT_Int16" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_int16_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_int16_type") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Word8) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_int16_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Int16)))))

data SAM_V1_6_Alignment_BOPT_Word16

cCsSiIf of the last optional field (type B). See section 1.5 of the SAM v1.6 specification documentation.

Constructors

SAM_V1_6_Alignment_BOPT_Word16

Fields

• sam_v1_6_alignment_bopt_word16_tag :: Seq Word8
• sam_v1_6_alignment_bopt_word16_type :: Word8
• sam_v1_6_alignment_bopt_word16_value :: Seq Word16

Instances

Generic SAM_V1_6_Alignment_BOPT_Word16

Defined in Data.SAM.Version1_6.Alignment.BOPT

Associated Types

type Rep SAM_V1_6_Alignment_BOPT_Word16 :: Type -> Type

Methods

from :: SAM_V1_6_Alignment_BOPT_Word16 -> Rep SAM_V1_6_Alignment_BOPT_Word16 x

to :: Rep SAM_V1_6_Alignment_BOPT_Word16 x -> SAM_V1_6_Alignment_BOPT_Word16

Show SAM_V1_6_Alignment_BOPT_Word16

Defined in Data.SAM.Version1_6.Alignment.BOPT

Methods

showsPrec :: Int -> SAM_V1_6_Alignment_BOPT_Word16 -> ShowS

show :: SAM_V1_6_Alignment_BOPT_Word16 -> String

showList :: [SAM_V1_6_Alignment_BOPT_Word16] -> ShowS

Eq SAM_V1_6_Alignment_BOPT_Word16

Defined in Data.SAM.Version1_6.Alignment.BOPT

Methods

(==) :: SAM_V1_6_Alignment_BOPT_Word16 -> SAM_V1_6_Alignment_BOPT_Word16 -> Bool

(/=) :: SAM_V1_6_Alignment_BOPT_Word16 -> SAM_V1_6_Alignment_BOPT_Word16 -> Bool

type Rep SAM_V1_6_Alignment_BOPT_Word16

Defined in Data.SAM.Version1_6.Alignment.BOPT

type Rep SAM_V1_6_Alignment_BOPT_Word16 = D1 ('MetaData "SAM_V1_6_Alignment_BOPT_Word16" "Data.SAM.Version1_6.Alignment.BOPT" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Alignment_BOPT_Word16" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_word16_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_word16_type") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Word8) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_word16_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word16)))))

data SAM_V1_6_Alignment_BOPT_Int32

cCsSiIf of the last optional field (type B). See section 1.5 of the SAM v1.6 specification documentation.

Constructors

SAM_V1_6_Alignment_BOPT_Int32

Fields

• sam_v1_6_alignment_bopt_int32_tag :: Seq Word8
• sam_v1_6_alignment_bopt_int32_type :: Word8
• sam_v1_6_alignment_bopt_int32_value :: Seq Int32

Instances

Generic SAM_V1_6_Alignment_BOPT_Int32

Defined in Data.SAM.Version1_6.Alignment.BOPT

Associated Types

type Rep SAM_V1_6_Alignment_BOPT_Int32 :: Type -> Type

Methods

from :: SAM_V1_6_Alignment_BOPT_Int32 -> Rep SAM_V1_6_Alignment_BOPT_Int32 x

to :: Rep SAM_V1_6_Alignment_BOPT_Int32 x -> SAM_V1_6_Alignment_BOPT_Int32

Show SAM_V1_6_Alignment_BOPT_Int32

Defined in Data.SAM.Version1_6.Alignment.BOPT

Methods

showsPrec :: Int -> SAM_V1_6_Alignment_BOPT_Int32 -> ShowS

show :: SAM_V1_6_Alignment_BOPT_Int32 -> String

showList :: [SAM_V1_6_Alignment_BOPT_Int32] -> ShowS

Eq SAM_V1_6_Alignment_BOPT_Int32

Defined in Data.SAM.Version1_6.Alignment.BOPT

Methods

(==) :: SAM_V1_6_Alignment_BOPT_Int32 -> SAM_V1_6_Alignment_BOPT_Int32 -> Bool

(/=) :: SAM_V1_6_Alignment_BOPT_Int32 -> SAM_V1_6_Alignment_BOPT_Int32 -> Bool

type Rep SAM_V1_6_Alignment_BOPT_Int32

Defined in Data.SAM.Version1_6.Alignment.BOPT

type Rep SAM_V1_6_Alignment_BOPT_Int32 = D1 ('MetaData "SAM_V1_6_Alignment_BOPT_Int32" "Data.SAM.Version1_6.Alignment.BOPT" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Alignment_BOPT_Int32" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_int32_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_int32_type") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Word8) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_int32_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Int32)))))

data SAM_V1_6_Alignment_BOPT_Word32

cCsSiIf of the last optional field (type B). See section 1.5 of the SAM v1.6 specification documentation.

Constructors

SAM_V1_6_Alignment_BOPT_Word32

Fields

• sam_v1_6_alignment_bopt_word32_tag :: Seq Word8
• sam_v1_6_alignment_bopt_word32_type :: Word8
• sam_v1_6_alignment_bopt_word32_value :: Seq Word32

Instances

Generic SAM_V1_6_Alignment_BOPT_Word32

Defined in Data.SAM.Version1_6.Alignment.BOPT

Associated Types

type Rep SAM_V1_6_Alignment_BOPT_Word32 :: Type -> Type

Methods

from :: SAM_V1_6_Alignment_BOPT_Word32 -> Rep SAM_V1_6_Alignment_BOPT_Word32 x

to :: Rep SAM_V1_6_Alignment_BOPT_Word32 x -> SAM_V1_6_Alignment_BOPT_Word32

Show SAM_V1_6_Alignment_BOPT_Word32

Defined in Data.SAM.Version1_6.Alignment.BOPT

Methods

showsPrec :: Int -> SAM_V1_6_Alignment_BOPT_Word32 -> ShowS

show :: SAM_V1_6_Alignment_BOPT_Word32 -> String

showList :: [SAM_V1_6_Alignment_BOPT_Word32] -> ShowS

Eq SAM_V1_6_Alignment_BOPT_Word32

Defined in Data.SAM.Version1_6.Alignment.BOPT

Methods

(==) :: SAM_V1_6_Alignment_BOPT_Word32 -> SAM_V1_6_Alignment_BOPT_Word32 -> Bool

(/=) :: SAM_V1_6_Alignment_BOPT_Word32 -> SAM_V1_6_Alignment_BOPT_Word32 -> Bool

type Rep SAM_V1_6_Alignment_BOPT_Word32

Defined in Data.SAM.Version1_6.Alignment.BOPT

type Rep SAM_V1_6_Alignment_BOPT_Word32 = D1 ('MetaData "SAM_V1_6_Alignment_BOPT_Word32" "Data.SAM.Version1_6.Alignment.BOPT" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Alignment_BOPT_Word32" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_word32_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: (S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_word32_type") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Word8) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt_word32_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word32)))))