Copyright | (c) Matthew Mosior 2023 |
---|---|
License | BSD-style |
Maintainer | mattm.github@gmail.com |
Portability | portable |
Safe Haskell | Safe-Inferred |
Language | Haskell2010 |
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_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
- data SAM_V1_6_Read_Group_Identifier = SAM_V1_6_Read_Group_Identifier {}
- data SAM_V1_6_Read_Group_Barcode_Sequence = SAM_V1_6_Read_Group_Barcode_Sequence {}
- data SAM_V1_6_Read_Group_Sequencing_Center = SAM_V1_6_Read_Group_Sequencing_Center {}
- data SAM_V1_6_Read_Group_Description = SAM_V1_6_Read_Group_Description {}
- data SAM_V1_6_Read_Group_Run_Date = SAM_V1_6_Read_Group_Run_Date {}
- data SAM_V1_6_Read_Group_Flow_Order = SAM_V1_6_Read_Group_Flow_Order {}
- data SAM_V1_6_Read_Group_Key_Sequence = SAM_V1_6_Read_Group_Key_Sequence {}
- data SAM_V1_6_Read_Group_Library = SAM_V1_6_Read_Group_Library {}
- data SAM_V1_6_Read_Group_Programs = SAM_V1_6_Read_Group_Programs {}
- data SAM_V1_6_Read_Group_Predicted_Median_Insert_Size = SAM_V1_6_Read_Group_Predicted_Median_Insert_Size {}
- data SAM_V1_6_Read_Group_Platform = SAM_V1_6_Read_Group_Platform {}
- data SAM_V1_6_Read_Group_Platform_Model = SAM_V1_6_Read_Group_Platform_Model {}
- data SAM_V1_6_Read_Group_Platform_Unit = SAM_V1_6_Read_Group_Platform_Unit {}
- data 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 # |
SAM version 1.6 Read group data types
data 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-0.3.1.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Read_Group_Identifier" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_identifer_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_read_group_identifer_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data 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-0.3.1.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Read_Group_Barcode_Sequence" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_barcode_sequence_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_read_group_barcode_sequence_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data 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-0.3.1.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Read_Group_Sequencing_Center" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_sequencing_center_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_read_group_sequencing_center_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data 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-0.3.1.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Read_Group_Description" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_description_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_read_group_description_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data SAM_V1_6_Read_Group_Run_Date Source #
DT tag for SAM_V1_6_Read_Group
.
Instances
data 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-0.3.1.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Read_Group_Flow_Order" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_flow_order_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_read_group_flow_order_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data 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-0.3.1.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Read_Group_Key_Sequence" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_key_sequence_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_read_group_key_sequence_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data 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-0.3.1.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Read_Group_Library" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_library_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_read_group_library_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data SAM_V1_6_Read_Group_Programs Source #
PG tag for SAM_V1_6_Read_Group
.
Instances
data SAM_V1_6_Read_Group_Predicted_Median_Insert_Size Source #
PI tag for SAM_V1_6_Read_Group
.
Instances
data SAM_V1_6_Read_Group_Platform Source #
PL tag for SAM_V1_6_Read_Group
.
Instances
data 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-0.3.1.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Read_Group_Platform_Model" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_platform_model_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_read_group_platform_model_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data 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-0.3.1.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Read_Group_Platform_Unit" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_read_group_platform_unit_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_read_group_platform_unit_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data SAM_V1_6_Read_Group_Sample Source #
SM tag for SAM_V1_6_Read_Group
.