{-# LANGUAGE DeriveDataTypeable #-} {-# LANGUAGE DeriveGeneric #-} {-# LANGUAGE FlexibleContexts #-} {-# LANGUAGE FlexibleInstances #-} {-# LANGUAGE MultiParamTypeClasses #-} {-# LANGUAGE OverloadedLists #-} {-# LANGUAGE OverloadedStrings #-} {-# LANGUAGE PackageImports #-} {-# LANGUAGE RecordWildCards #-} {-# LANGUAGE TemplateHaskell #-} {-# LANGUAGE TypeFamilies #-} {-# Language QuasiQuotes #-} -- | -- Module : Data.SAM.Version1_6.Header.RG -- Copyright : (c) Matthew Mosior 2023 -- License : BSD-style -- Maintainer : mattm.github@gmail.com -- Portability : portable -- -- = 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](https://hackage.haskell.org/package/containers) library -- for the above warning text. -- -- = Description -- -- This library enables the decoding/encoding of SAM, BAM and CRAM file formats. module Data.SAM.Version1_6.Header.RG ( -- * SAM version 1.6 Read group data type SAM_V1_6_Read_Group(..), -- * SAM version 1.6 Read group data types SAM_V1_6_Read_Group_Identifier(..), SAM_V1_6_Read_Group_Barcode_Sequence(..), SAM_V1_6_Read_Group_Sequencing_Center(..), SAM_V1_6_Read_Group_Description(..), SAM_V1_6_Read_Group_Run_Date(..), SAM_V1_6_Read_Group_Flow_Order(..), SAM_V1_6_Read_Group_Key_Sequence(..), SAM_V1_6_Read_Group_Library(..), SAM_V1_6_Read_Group_Programs(..), SAM_V1_6_Read_Group_Predicted_Median_Insert_Size(..), SAM_V1_6_Read_Group_Platform(..), SAM_V1_6_Read_Group_Platform_Model(..), SAM_V1_6_Read_Group_Platform_Unit(..), SAM_V1_6_Read_Group_Sample(..) ) where import Data.ByteString import Data.Data import Data.Sequence import Data.Word import Generics.Deriving.Base -- | Custom SAM (version 1.6) @"SAM_V1_6_Read_Group"@ data type. -- See section 1.3 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation. 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 } -- | ID tag for @"SAM_V1_6_Read_Group"@. data SAM_V1_6_Read_Group_Identifier = SAM_V1_6_Read_Group_Identifier { sam_v1_6_read_group_identifer_tag :: Seq Word8 , sam_v1_6_read_group_identifer_value :: ByteString } deriving (Generic,Typeable) -- | Eq instance for @"SAM_V1_6_Read_Group_Identifier"@. instance Eq SAM_V1_6_Read_Group_Identifier where SAM_V1_6_Read_Group_Identifier sam_v1_6_read_group_identifier_tag1 sam_v1_6_read_group_identifier_value1 == SAM_V1_6_Read_Group_Identifier sam_v1_6_read_group_identifier_tag2 sam_v1_6_read_group_identifier_value2 = sam_v1_6_read_group_identifier_tag1 == sam_v1_6_read_group_identifier_tag2 && sam_v1_6_read_group_identifier_value1 == sam_v1_6_read_group_identifier_value2 -- | Show instance for @"SAM_V1_6_Read_Group_Identifier"@. instance Show SAM_V1_6_Read_Group_Identifier where show (SAM_V1_6_Read_Group_Identifier tag value) = "SAM_V1_6_Read_Group_Identifier { " ++ "tag = " ++ (show tag) ++ " , value = " ++ (show value) ++ " }" -- | BC tag for @"SAM_V1_6_Read_Group"@. data SAM_V1_6_Read_Group_Barcode_Sequence = SAM_V1_6_Read_Group_Barcode_Sequence { sam_v1_6_read_group_barcode_sequence_tag :: Seq Word8 , sam_v1_6_read_group_barcode_sequence_value :: ByteString } deriving (Generic,Typeable) -- | Eq instance for @"SAM_V1_6_Read_Group_Barcode_Sequence"@. instance Eq SAM_V1_6_Read_Group_Barcode_Sequence where SAM_V1_6_Read_Group_Barcode_Sequence sam_v1_6_read_group_barcode_sequence_tag1 sam_v1_6_read_group_barcode_sequence_value1 == SAM_V1_6_Read_Group_Barcode_Sequence sam_v1_6_read_group_barcode_sequence_tag2 sam_v1_6_read_group_barcode_sequence_value2 = sam_v1_6_read_group_barcode_sequence_tag1 == sam_v1_6_read_group_barcode_sequence_tag2 && sam_v1_6_read_group_barcode_sequence_value1 == sam_v1_6_read_group_barcode_sequence_value2 -- | Show instance for @"SAM_V1_6_Read_Group_Barcode_Sequence"@. instance Show SAM_V1_6_Read_Group_Barcode_Sequence where show (SAM_V1_6_Read_Group_Barcode_Sequence tag value) = "SAM_V1_6_Read_Group_Barcode_Sequence { " ++ "tag = " ++ (show tag) ++ " , value = " ++ (show value) ++ " }" -- | CN tag for @"SAM_V1_6_Read_Group"@. data SAM_V1_6_Read_Group_Sequencing_Center = SAM_V1_6_Read_Group_Sequencing_Center { sam_v1_6_read_group_sequencing_center_tag :: Seq Word8 , sam_v1_6_read_group_sequencing_center_value :: ByteString } deriving (Generic,Typeable) -- | Eq instance for @"SAM_V1_6_Read_Group_Sequencing_Center"@. instance Eq SAM_V1_6_Read_Group_Sequencing_Center where SAM_V1_6_Read_Group_Sequencing_Center sam_v1_6_read_group_sequencing_center_tag1 sam_v1_6_read_group_sequencing_center_value1 == SAM_V1_6_Read_Group_Sequencing_Center sam_v1_6_read_group_sequencing_center_tag2 sam_v1_6_read_group_sequencing_center_value2 = sam_v1_6_read_group_sequencing_center_tag1 == sam_v1_6_read_group_sequencing_center_tag2 && sam_v1_6_read_group_sequencing_center_value1 == sam_v1_6_read_group_sequencing_center_value2 -- | Show instance for @"SAM_V1_6_Read_Group_Sequencing_Center"@. instance Show SAM_V1_6_Read_Group_Sequencing_Center where show (SAM_V1_6_Read_Group_Sequencing_Center tag value) = "SAM_V1_6_Read_Group_Sequencing_Center { " ++ "tag = " ++ (show tag) ++ " , value = " ++ (show value) ++ " }" -- | DS tag for @"SAM_V1_6_Read_Group"@. data SAM_V1_6_Read_Group_Description = SAM_V1_6_Read_Group_Description { sam_v1_6_read_group_description_tag :: Seq Word8 , sam_v1_6_read_group_description_value :: ByteString } deriving (Generic,Typeable) -- | Eq instance for @"SAM_V1_6_Read_Group_Description"@. instance Eq SAM_V1_6_Read_Group_Description where SAM_V1_6_Read_Group_Description sam_v1_6_read_group_description_tag1 sam_v1_6_read_group_description_value1 == SAM_V1_6_Read_Group_Description sam_v1_6_read_group_description_tag2 sam_v1_6_read_group_description_value2 = sam_v1_6_read_group_description_tag1 == sam_v1_6_read_group_description_tag2 && sam_v1_6_read_group_description_value1 == sam_v1_6_read_group_description_value2 -- | Show instance for @"SAM_V1_6_Read_Group_Description"@. instance Show SAM_V1_6_Read_Group_Description where show (SAM_V1_6_Read_Group_Description tag value) = "SAM_V1_6_Read_Group_Description { " ++ "tag = " ++ (show tag) ++ " , value = " ++ (show value) ++ " }" -- | DT tag for @"SAM_V1_6_Read_Group"@. data SAM_V1_6_Read_Group_Run_Date = SAM_V1_6_Read_Group_Run_Date { sam_v1_6_read_group_run_date_tag :: Seq Word8 , sam_v1_6_read_group_run_date_value :: ByteString } deriving (Generic,Typeable) -- | Eq instance for @"SAM_V1_6_Read_Group_Run_Date"@. instance Eq SAM_V1_6_Read_Group_Run_Date where SAM_V1_6_Read_Group_Run_Date sam_v1_6_read_group_run_date_tag1 sam_v1_6_read_group_run_date_value1 == SAM_V1_6_Read_Group_Run_Date sam_v1_6_read_group_run_date_tag2 sam_v1_6_read_group_run_date_value2 = sam_v1_6_read_group_run_date_tag1 == sam_v1_6_read_group_run_date_tag2 && sam_v1_6_read_group_run_date_value1 == sam_v1_6_read_group_run_date_value2 -- | Show instance for @"SAM_V1_6_Read_Group_Run_Date"@. instance Show SAM_V1_6_Read_Group_Run_Date where show (SAM_V1_6_Read_Group_Run_Date tag value) = "SAM_V1_6_Read_Group_Run_Date { " ++ "tag = " ++ (show tag) ++ " , value = " ++ (show value) ++ " }" -- | FO tag for @"SAM_V1_6_Read_Group"@. data SAM_V1_6_Read_Group_Flow_Order = SAM_V1_6_Read_Group_Flow_Order { sam_v1_6_read_group_flow_order_tag :: Seq Word8 , sam_v1_6_read_group_flow_order_value :: ByteString } deriving (Generic,Typeable) -- | Eq instance for @"SAM_V1_6_Read_Group_Flow_Order"@. instance Eq SAM_V1_6_Read_Group_Flow_Order where SAM_V1_6_Read_Group_Flow_Order sam_v1_6_read_group_flow_order_tag1 sam_v1_6_one_line_comment_value1 == SAM_V1_6_Read_Group_Flow_Order sam_v1_6_read_group_flow_order_tag2 sam_v1_6_read_group_flow_order_value2 = sam_v1_6_read_group_flow_order_tag1 == sam_v1_6_read_group_flow_order_tag2 && sam_v1_6_one_line_comment_value1 == sam_v1_6_read_group_flow_order_value2 -- | Show instance for @"SAM_V1_6_Read_Group_Flow_Order"@. instance Show SAM_V1_6_Read_Group_Flow_Order where show (SAM_V1_6_Read_Group_Flow_Order tag value) = "SAM_V1_6_Read_Group_Flow_Order { " ++ "tag = " ++ (show tag) ++ " , value = " ++ (show value) ++ " }" -- | KS tag for @"SAM_V1_6_Read_Group"@. data SAM_V1_6_Read_Group_Key_Sequence = SAM_V1_6_Read_Group_Key_Sequence { sam_v1_6_read_group_key_sequence_tag :: Seq Word8 , sam_v1_6_read_group_key_sequence_value :: ByteString } deriving (Generic,Typeable) -- | Eq instance for @"SAM_V1_6_Read_Group_Key_Sequence"@. instance Eq SAM_V1_6_Read_Group_Key_Sequence where SAM_V1_6_Read_Group_Key_Sequence sam_v1_6_read_group_key_sequence_tag1 sam_v1_6_read_group_key_sequence_value1 == SAM_V1_6_Read_Group_Key_Sequence sam_v1_6_read_group_key_sequence_tag2 sam_v1_6_read_group_key_sequence_value2 = sam_v1_6_read_group_key_sequence_tag1 == sam_v1_6_read_group_key_sequence_tag2 && sam_v1_6_read_group_key_sequence_value1 == sam_v1_6_read_group_key_sequence_value2 -- | Show instance for @"SAM_V1_6_Read_Group_Key_Sequence"@. instance Show SAM_V1_6_Read_Group_Key_Sequence where show (SAM_V1_6_Read_Group_Key_Sequence tag value) = "SAM_V1_6_Read_Group_Key_Sequence { " ++ "tag = " ++ (show tag) ++ " , value = " ++ (show value) ++ " }" -- | LB tag for @"SAM_V1_6_Read_Group"@. data SAM_V1_6_Read_Group_Library = SAM_V1_6_Read_Group_Library { sam_v1_6_read_group_library_tag :: Seq Word8 , sam_v1_6_read_group_library_value :: ByteString } deriving (Generic,Typeable) -- | Eq instance for @"SAM_V1_6_Read_Group_Library"@. instance Eq SAM_V1_6_Read_Group_Library where SAM_V1_6_Read_Group_Library sam_v1_6_read_group_library_tag1 sam_v1_6_read_group_library_value1 == SAM_V1_6_Read_Group_Library sam_v1_6_read_group_library_tag2 sam_v1_6_read_group_library_value2 = sam_v1_6_read_group_library_tag1 == sam_v1_6_read_group_library_tag2 && sam_v1_6_read_group_library_value1 == sam_v1_6_read_group_library_value2 -- | Show instance for @"SAM_V1_6_Read_Group_Library"@. instance Show SAM_V1_6_Read_Group_Library where show (SAM_V1_6_Read_Group_Library tag value) = "SAM_V1_6_Read_Group_Library { " ++ "tag = " ++ (show tag) ++ " , value = " ++ (show value) ++ " }" -- | PG tag for @"SAM_V1_6_Read_Group"@. data SAM_V1_6_Read_Group_Programs = SAM_V1_6_Read_Group_Programs { sam_v1_6_read_group_programs_tag :: Seq Word8 , sam_v1_6_read_group_programs_value :: ByteString } deriving (Generic,Typeable) -- | Eq instance for @"SAM_V1_6_Read_Group_Programs"@. instance Eq SAM_V1_6_Read_Group_Programs where SAM_V1_6_Read_Group_Programs sam_v1_6_read_group_programs_tag1 sam_v1_6_read_group_programs_value1 == SAM_V1_6_Read_Group_Programs sam_v1_6_read_group_programs_tag2 sam_v1_6_read_group_programs_value2 = sam_v1_6_read_group_programs_tag1 == sam_v1_6_read_group_programs_tag2 && sam_v1_6_read_group_programs_value1 == sam_v1_6_read_group_programs_value2 -- | Show instance for @"SAM_V1_6_Read_Group_Programs"@. instance Show SAM_V1_6_Read_Group_Programs where show (SAM_V1_6_Read_Group_Programs tag value) = "SAM_V1_6_Read_Group_Programs { " ++ "tag = " ++ (show tag) ++ " , value = " ++ (show value) ++ " }" -- | PI tag for @"SAM_V1_6_Read_Group"@. data SAM_V1_6_Read_Group_Predicted_Median_Insert_Size = SAM_V1_6_Read_Group_Predicted_Median_Insert_Size { sam_v1_6_read_group_predicted_median_insert_size_tag :: Seq Word8 , sam_v1_6_read_group_predicted_median_insert_size_value :: ByteString } deriving (Generic,Typeable) -- | Eq instance for @"SAM_V1_6_Read_Group_Predicted_Median_Insert_Size"@. instance Eq SAM_V1_6_Read_Group_Predicted_Median_Insert_Size where SAM_V1_6_Read_Group_Predicted_Median_Insert_Size sam_v1_6_read_group_predicted_median_insert_size_tag1 sam_v1_6_one_line_comment_value1 == SAM_V1_6_Read_Group_Predicted_Median_Insert_Size sam_v1_6_read_group_predicted_median_insert_size_tag2 sam_v1_6_read_group_predicted_median_insert_size_value2 = sam_v1_6_read_group_predicted_median_insert_size_tag1 == sam_v1_6_read_group_predicted_median_insert_size_tag2 && sam_v1_6_one_line_comment_value1 == sam_v1_6_read_group_predicted_median_insert_size_value2 -- | Show instance for @"SAM_V1_6_Read_Group_Predicted_Median_Insert_Size"@. instance Show SAM_V1_6_Read_Group_Predicted_Median_Insert_Size where show (SAM_V1_6_Read_Group_Predicted_Median_Insert_Size tag value) = "SAM_V1_6_Read_Group_Predicted_Median_Insert_Size { " ++ "tag = " ++ (show tag) ++ " , value = " ++ (show value) ++ " }" -- | PL tag for @"SAM_V1_6_Read_Group"@. data SAM_V1_6_Read_Group_Platform = SAM_V1_6_Read_Group_Platform { sam_v1_6_read_group_platform_tag :: Seq Word8 , sam_v1_6_read_group_platform_value :: ByteString } deriving (Generic,Typeable) -- | Eq instance for @"SAM_V1_6_Read_Group_Platform"@. instance Eq SAM_V1_6_Read_Group_Platform where SAM_V1_6_Read_Group_Platform sam_v1_6_read_group_platform_tag1 sam_v1_6_read_group_platform_value1 == SAM_V1_6_Read_Group_Platform sam_v1_6_read_group_platform_tag2 sam_v1_6_read_group_platform_value2 = sam_v1_6_read_group_platform_tag1 == sam_v1_6_read_group_platform_tag2 && sam_v1_6_read_group_platform_value1 == sam_v1_6_read_group_platform_value2 -- | Show instance for @"SAM_V1_6_Read_Group_Platform"@. instance Show SAM_V1_6_Read_Group_Platform where show (SAM_V1_6_Read_Group_Platform tag value) = "SAM_V1_6_Read_Group_Platform { " ++ "tag = " ++ (show tag) ++ " , value = " ++ (show value) ++ " }" -- | PM tag for @"SAM_V1_6_Read_Group"@. data SAM_V1_6_Read_Group_Platform_Model = SAM_V1_6_Read_Group_Platform_Model { sam_v1_6_read_group_platform_model_tag :: Seq Word8 , sam_v1_6_read_group_platform_model_value :: ByteString } deriving (Generic,Typeable) -- | Eq instance for @"SAM_V1_6_Read_Group_Platform_Model"@. instance Eq SAM_V1_6_Read_Group_Platform_Model where SAM_V1_6_Read_Group_Platform_Model sam_v1_6_read_group_platform_model_tag1 sam_v1_6_read_group_platform_model_value1 == SAM_V1_6_Read_Group_Platform_Model sam_v1_6_read_group_platform_model_tag2 sam_v1_6_read_group_platform_model_value2 = sam_v1_6_read_group_platform_model_tag1 == sam_v1_6_read_group_platform_model_tag2 && sam_v1_6_read_group_platform_model_value1 == sam_v1_6_read_group_platform_model_value2 -- | Show instance for @"SAM_V1_6_Read_Group_Platform_Model"@. instance Show SAM_V1_6_Read_Group_Platform_Model where show (SAM_V1_6_Read_Group_Platform_Model tag value) = "SAM_V1_6_Read_Group_Platform_Model { " ++ "tag = " ++ (show tag) ++ " , value = " ++ (show value) ++ " }" -- | PU tag for @"SAM_V1_6_Read_Group"@. data SAM_V1_6_Read_Group_Platform_Unit = SAM_V1_6_Read_Group_Platform_Unit { sam_v1_6_read_group_platform_unit_tag :: Seq Word8 , sam_v1_6_read_group_platform_unit_value :: ByteString } deriving (Generic,Typeable) -- | Eq instance for @"SAM_V1_6_Read_Group_Platform_Unit"@. instance Eq SAM_V1_6_Read_Group_Platform_Unit where SAM_V1_6_Read_Group_Platform_Unit sam_v1_6_read_group_platform_unit_tag1 sam_v1_6_read_group_platform_unit_value1 == SAM_V1_6_Read_Group_Platform_Unit sam_v1_6_read_group_platform_unit_tag2 sam_v1_6_read_group_platform_unit_value2 = sam_v1_6_read_group_platform_unit_tag1 == sam_v1_6_read_group_platform_unit_tag2 && sam_v1_6_read_group_platform_unit_value1 == sam_v1_6_read_group_platform_unit_value2 -- | Show instance for @"SAM_V1_6_Read_Group_Platform_Unit"@. instance Show SAM_V1_6_Read_Group_Platform_Unit where show (SAM_V1_6_Read_Group_Platform_Unit tag value) = "SAM_V1_6_Read_Group_Platform_Unit { " ++ "tag = " ++ (show tag) ++ " , value = " ++ (show value) ++ " }" -- | SM tag for @"SAM_V1_6_Read_Group"@. data SAM_V1_6_Read_Group_Sample = SAM_V1_6_Read_Group_Sample { sam_v1_6_read_group_sample_tag :: Seq Word8 , sam_v1_6_read_group_sample_value :: ByteString } deriving (Generic,Typeable) -- | Eq instance for @"SAM_V1_6_Read_Group_Sample"@. instance Eq SAM_V1_6_Read_Group_Sample where SAM_V1_6_Read_Group_Sample sam_v1_6_read_group_sample_tag1 sam_v1_6_read_group_sample_value1 == SAM_V1_6_Read_Group_Sample sam_v1_6_read_group_sample_tag2 sam_v1_6_read_group_sample_value2 = sam_v1_6_read_group_sample_tag1 == sam_v1_6_read_group_sample_tag2 && sam_v1_6_read_group_sample_value1 == sam_v1_6_read_group_sample_value2 -- | Show instance for @"SAM_V1_6_Read_Group_Sample"@. instance Show SAM_V1_6_Read_Group_Sample where show (SAM_V1_6_Read_Group_Sample tag value) = "SAM_V1_6_Read_Group_Sample { " ++ "tag = " ++ (show tag) ++ " , value = " ++ (show value) ++ " }"