Copyright | (c) Matthew Mosior 2023 |
---|---|
License | BSD-style |
Maintainer | mattm.github@gmail.com |
Portability | portable |
Safe Haskell | Safe-Inferred |
Language | Haskell2010 |
Description
This library enables the decoding/encoding of SAM, BAM and CRAM file formats.
Synopsis
- data SAM_V1_6_Read_Group = SAM_V1_6_Read_Group {
- sam_v1_6_read_group_identifer :: SAM_V1_6_Read_Group_Identifier
- sam_v1_6_read_group_barcode_sequence :: Maybe SAM_V1_6_Read_Group_Barcode_Sequence
- sam_v1_6_read_group_sequencing_center :: Maybe SAM_V1_6_Read_Group_Sequencing_Center
- sam_v1_6_read_group_description :: Maybe SAM_V1_6_Read_Group_Description
- sam_v1_6_read_group_run_date :: Maybe SAM_V1_6_Read_Group_Run_Date
- sam_v1_6_read_group_flow_order :: Maybe SAM_V1_6_Read_Group_Flow_Order
- sam_v1_6_read_group_key_sequence :: Maybe SAM_V1_6_Read_Group_Key_Sequence
- sam_v1_6_read_group_library :: Maybe SAM_V1_6_Read_Group_Library
- sam_v1_6_read_group_programs :: Maybe SAM_V1_6_Read_Group_Programs
- sam_v1_6_read_group_predicted_median_insert_size :: Maybe SAM_V1_6_Read_Group_Predicted_Median_Insert_Size
- sam_v1_6_read_group_platform :: Maybe SAM_V1_6_Read_Group_Platform
- sam_v1_6_read_group_platform_model :: Maybe SAM_V1_6_Read_Group_Platform_Model
- sam_v1_6_read_group_platform_unit :: Maybe SAM_V1_6_Read_Group_Platform_Unit
- sam_v1_6_read_group_sample :: Maybe SAM_V1_6_Read_Group_Sample
- newtype SAM_V1_6_Read_Group_Identifier = SAM_V1_6_Read_Group_Identifier {}
- newtype SAM_V1_6_Read_Group_Barcode_Sequence = SAM_V1_6_Read_Group_Barcode_Sequence {}
- newtype SAM_V1_6_Read_Group_Sequencing_Center = SAM_V1_6_Read_Group_Sequencing_Center {}
- newtype SAM_V1_6_Read_Group_Description = SAM_V1_6_Read_Group_Description {}
- newtype SAM_V1_6_Read_Group_Run_Date = SAM_V1_6_Read_Group_Run_Date {}
- newtype SAM_V1_6_Read_Group_Flow_Order = SAM_V1_6_Read_Group_Flow_Order {}
- newtype SAM_V1_6_Read_Group_Key_Sequence = SAM_V1_6_Read_Group_Key_Sequence {}
- newtype SAM_V1_6_Read_Group_Library = SAM_V1_6_Read_Group_Library {}
- newtype SAM_V1_6_Read_Group_Programs = SAM_V1_6_Read_Group_Programs {}
- newtype SAM_V1_6_Read_Group_Predicted_Median_Insert_Size = SAM_V1_6_Read_Group_Predicted_Median_Insert_Size {}
- newtype SAM_V1_6_Read_Group_Platform = SAM_V1_6_Read_Group_Platform {}
- newtype SAM_V1_6_Read_Group_Platform_Model = SAM_V1_6_Read_Group_Platform_Model {}
- newtype SAM_V1_6_Read_Group_Platform_Unit = SAM_V1_6_Read_Group_Platform_Unit {}
- newtype SAM_V1_6_Read_Group_Sample = SAM_V1_6_Read_Group_Sample {}
SAM version 1.6 Read group data type
data SAM_V1_6_Read_Group Source #
Custom SAM (version 1.6) SAM_V1_6_Read_Group
data type.
See section 1.3 of the SAM v1.6 specification documentation.
Instances
Show SAM_V1_6_Read_Group Source # | |
Defined in Data.SAM.Version1_6.Header.RG showsPrec :: Int -> SAM_V1_6_Read_Group -> ShowS # show :: SAM_V1_6_Read_Group -> String # showList :: [SAM_V1_6_Read_Group] -> ShowS # | |
Eq SAM_V1_6_Read_Group Source # | |
Defined in Data.SAM.Version1_6.Header.RG (==) :: SAM_V1_6_Read_Group -> SAM_V1_6_Read_Group -> Bool # (/=) :: SAM_V1_6_Read_Group -> SAM_V1_6_Read_Group -> Bool # |
SAM version 1.6 Read group data types
newtype SAM_V1_6_Read_Group_Identifier Source #
ID tag for SAM_V1_6_Read_Group
.
Instances
Generic SAM_V1_6_Read_Group_Identifier Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Identifier :: Type -> Type # | |
Show SAM_V1_6_Read_Group_Identifier Source # | |
Defined in Data.SAM.Version1_6.Header.RG | |
Eq SAM_V1_6_Read_Group_Identifier Source # | |
type Rep SAM_V1_6_Read_Group_Identifier Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Identifier = D1 ('MetaData "SAM_V1_6_Read_Group_Identifier" "Data.SAM.Version1_6.Header.RG" "hs-samtools-0.7.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Read_Group_Identifier" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_identifier_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Read_Group_Barcode_Sequence Source #
BC tag for SAM_V1_6_Read_Group
.
Instances
Generic SAM_V1_6_Read_Group_Barcode_Sequence Source # | |
Show SAM_V1_6_Read_Group_Barcode_Sequence Source # | |
Defined in Data.SAM.Version1_6.Header.RG | |
Eq SAM_V1_6_Read_Group_Barcode_Sequence Source # | |
type Rep SAM_V1_6_Read_Group_Barcode_Sequence Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Barcode_Sequence = D1 ('MetaData "SAM_V1_6_Read_Group_Barcode_Sequence" "Data.SAM.Version1_6.Header.RG" "hs-samtools-0.7.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Read_Group_Barcode_Sequence" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_barcode_sequence_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Read_Group_Sequencing_Center Source #
CN tag for SAM_V1_6_Read_Group
.
Instances
Generic SAM_V1_6_Read_Group_Sequencing_Center Source # | |
Show SAM_V1_6_Read_Group_Sequencing_Center Source # | |
Eq SAM_V1_6_Read_Group_Sequencing_Center Source # | |
type Rep SAM_V1_6_Read_Group_Sequencing_Center Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Sequencing_Center = D1 ('MetaData "SAM_V1_6_Read_Group_Sequencing_Center" "Data.SAM.Version1_6.Header.RG" "hs-samtools-0.7.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Read_Group_Sequencing_Center" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_sequencing_center_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Read_Group_Description Source #
DS tag for SAM_V1_6_Read_Group
.
Instances
Generic SAM_V1_6_Read_Group_Description Source # | |
Show SAM_V1_6_Read_Group_Description Source # | |
Defined in Data.SAM.Version1_6.Header.RG | |
Eq SAM_V1_6_Read_Group_Description Source # | |
type Rep SAM_V1_6_Read_Group_Description Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Description = D1 ('MetaData "SAM_V1_6_Read_Group_Description" "Data.SAM.Version1_6.Header.RG" "hs-samtools-0.7.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Read_Group_Description" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_description_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Read_Group_Run_Date Source #
DT tag for SAM_V1_6_Read_Group
.
Instances
Generic SAM_V1_6_Read_Group_Run_Date Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Run_Date :: Type -> Type # | |
Show SAM_V1_6_Read_Group_Run_Date Source # | |
Defined in Data.SAM.Version1_6.Header.RG showsPrec :: Int -> SAM_V1_6_Read_Group_Run_Date -> ShowS # show :: SAM_V1_6_Read_Group_Run_Date -> String # showList :: [SAM_V1_6_Read_Group_Run_Date] -> ShowS # | |
Eq SAM_V1_6_Read_Group_Run_Date Source # | |
type Rep SAM_V1_6_Read_Group_Run_Date Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Run_Date = D1 ('MetaData "SAM_V1_6_Read_Group_Run_Date" "Data.SAM.Version1_6.Header.RG" "hs-samtools-0.7.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Read_Group_Run_Date" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_run_date_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Read_Group_Flow_Order Source #
FO tag for SAM_V1_6_Read_Group
.
Instances
Generic SAM_V1_6_Read_Group_Flow_Order Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Flow_Order :: Type -> Type # | |
Show SAM_V1_6_Read_Group_Flow_Order Source # | |
Defined in Data.SAM.Version1_6.Header.RG | |
Eq SAM_V1_6_Read_Group_Flow_Order Source # | |
type Rep SAM_V1_6_Read_Group_Flow_Order Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Flow_Order = D1 ('MetaData "SAM_V1_6_Read_Group_Flow_Order" "Data.SAM.Version1_6.Header.RG" "hs-samtools-0.7.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Read_Group_Flow_Order" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_flow_order_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Read_Group_Key_Sequence Source #
KS tag for SAM_V1_6_Read_Group
.
Instances
Generic SAM_V1_6_Read_Group_Key_Sequence Source # | |
Show SAM_V1_6_Read_Group_Key_Sequence Source # | |
Defined in Data.SAM.Version1_6.Header.RG | |
Eq SAM_V1_6_Read_Group_Key_Sequence Source # | |
type Rep SAM_V1_6_Read_Group_Key_Sequence Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Key_Sequence = D1 ('MetaData "SAM_V1_6_Read_Group_Key_Sequence" "Data.SAM.Version1_6.Header.RG" "hs-samtools-0.7.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Read_Group_Key_Sequence" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_key_sequence_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Read_Group_Library Source #
LB tag for SAM_V1_6_Read_Group
.
Instances
Generic SAM_V1_6_Read_Group_Library Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Library :: Type -> Type # | |
Show SAM_V1_6_Read_Group_Library Source # | |
Defined in Data.SAM.Version1_6.Header.RG showsPrec :: Int -> SAM_V1_6_Read_Group_Library -> ShowS # show :: SAM_V1_6_Read_Group_Library -> String # showList :: [SAM_V1_6_Read_Group_Library] -> ShowS # | |
Eq SAM_V1_6_Read_Group_Library Source # | |
type Rep SAM_V1_6_Read_Group_Library Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Library = D1 ('MetaData "SAM_V1_6_Read_Group_Library" "Data.SAM.Version1_6.Header.RG" "hs-samtools-0.7.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Read_Group_Library" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_library_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Read_Group_Programs Source #
PG tag for SAM_V1_6_Read_Group
.
Instances
Generic SAM_V1_6_Read_Group_Programs Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Programs :: Type -> Type # | |
Show SAM_V1_6_Read_Group_Programs Source # | |
Defined in Data.SAM.Version1_6.Header.RG showsPrec :: Int -> SAM_V1_6_Read_Group_Programs -> ShowS # show :: SAM_V1_6_Read_Group_Programs -> String # showList :: [SAM_V1_6_Read_Group_Programs] -> ShowS # | |
Eq SAM_V1_6_Read_Group_Programs Source # | |
type Rep SAM_V1_6_Read_Group_Programs Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Programs = D1 ('MetaData "SAM_V1_6_Read_Group_Programs" "Data.SAM.Version1_6.Header.RG" "hs-samtools-0.7.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Read_Group_Programs" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_programs_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Read_Group_Predicted_Median_Insert_Size Source #
PI tag for SAM_V1_6_Read_Group
.
Instances
Generic SAM_V1_6_Read_Group_Predicted_Median_Insert_Size Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Predicted_Median_Insert_Size :: Type -> Type # | |
Show SAM_V1_6_Read_Group_Predicted_Median_Insert_Size Source # | |
Eq SAM_V1_6_Read_Group_Predicted_Median_Insert_Size Source # | |
type Rep SAM_V1_6_Read_Group_Predicted_Median_Insert_Size Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Predicted_Median_Insert_Size = D1 ('MetaData "SAM_V1_6_Read_Group_Predicted_Median_Insert_Size" "Data.SAM.Version1_6.Header.RG" "hs-samtools-0.7.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Read_Group_Predicted_Median_Insert_Size" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_predicted_median_insert_size_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Read_Group_Platform Source #
PL tag for SAM_V1_6_Read_Group
.
Instances
Generic SAM_V1_6_Read_Group_Platform Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Platform :: Type -> Type # | |
Show SAM_V1_6_Read_Group_Platform Source # | |
Defined in Data.SAM.Version1_6.Header.RG showsPrec :: Int -> SAM_V1_6_Read_Group_Platform -> ShowS # show :: SAM_V1_6_Read_Group_Platform -> String # showList :: [SAM_V1_6_Read_Group_Platform] -> ShowS # | |
Eq SAM_V1_6_Read_Group_Platform Source # | |
type Rep SAM_V1_6_Read_Group_Platform Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Platform = D1 ('MetaData "SAM_V1_6_Read_Group_Platform" "Data.SAM.Version1_6.Header.RG" "hs-samtools-0.7.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Read_Group_Platform" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_platform_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Read_Group_Platform_Model Source #
PM tag for SAM_V1_6_Read_Group
.
Instances
Generic SAM_V1_6_Read_Group_Platform_Model Source # | |
Show SAM_V1_6_Read_Group_Platform_Model Source # | |
Defined in Data.SAM.Version1_6.Header.RG | |
Eq SAM_V1_6_Read_Group_Platform_Model Source # | |
type Rep SAM_V1_6_Read_Group_Platform_Model Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Platform_Model = D1 ('MetaData "SAM_V1_6_Read_Group_Platform_Model" "Data.SAM.Version1_6.Header.RG" "hs-samtools-0.7.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Read_Group_Platform_Model" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_platform_model_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Read_Group_Platform_Unit Source #
PU tag for SAM_V1_6_Read_Group
.
Instances
Generic SAM_V1_6_Read_Group_Platform_Unit Source # | |
Show SAM_V1_6_Read_Group_Platform_Unit Source # | |
Defined in Data.SAM.Version1_6.Header.RG | |
Eq SAM_V1_6_Read_Group_Platform_Unit Source # | |
type Rep SAM_V1_6_Read_Group_Platform_Unit Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Platform_Unit = D1 ('MetaData "SAM_V1_6_Read_Group_Platform_Unit" "Data.SAM.Version1_6.Header.RG" "hs-samtools-0.7.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Read_Group_Platform_Unit" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_platform_unit_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Read_Group_Sample Source #
SM tag for SAM_V1_6_Read_Group
.
Instances
Generic SAM_V1_6_Read_Group_Sample Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Sample :: Type -> Type # | |
Show SAM_V1_6_Read_Group_Sample Source # | |
Defined in Data.SAM.Version1_6.Header.RG showsPrec :: Int -> SAM_V1_6_Read_Group_Sample -> ShowS # show :: SAM_V1_6_Read_Group_Sample -> String # showList :: [SAM_V1_6_Read_Group_Sample] -> ShowS # | |
Eq SAM_V1_6_Read_Group_Sample Source # | |
Defined in Data.SAM.Version1_6.Header.RG | |
type Rep SAM_V1_6_Read_Group_Sample Source # | |
Defined in Data.SAM.Version1_6.Header.RG type Rep SAM_V1_6_Read_Group_Sample = D1 ('MetaData "SAM_V1_6_Read_Group_Sample" "Data.SAM.Version1_6.Header.RG" "hs-samtools-0.7.0.0-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Read_Group_Sample" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_sample_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |