{-# 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.PG
-- 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.PG ( -- * SAM version 1.6 program data type
                                       SAM_V1_6_Program(..),
                                       -- * SAM version 1.6 program data types
                                       SAM_V1_6_Program_Record_Identifier(..),
                                       SAM_V1_6_Program_Name(..),
                                       SAM_V1_6_Program_Command_Line(..),
                                       SAM_V1_6_Program_Previous_PG_ID(..),
                                       SAM_V1_6_Program_Description(..),
                                       SAM_V1_6_Program_Version(..)
                                     ) where

import Data.ByteString
import Data.Sequence
import Data.Word


-- | Custom SAM (version 1.6) @"SAM_V1_6_Program"@ 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_Program = SAM_V1_6_Program { sam_v1_6_program_record_identifier :: SAM_V1_6_Program_Record_Identifier
                                         , sam_v1_6_program_name              :: Maybe SAM_V1_6_Program_Name
                                         , sam_v1_6_program_command_line      :: Maybe SAM_V1_6_Program_Command_Line
                                         , sam_v1_6_program_previous_pg_id    :: Maybe SAM_V1_6_Program_Previous_PG_ID
                                         , sam_v1_6_program_description       :: Maybe SAM_V1_6_Program_Description
                                         , sam_v1_6_program_version           :: Maybe SAM_V1_6_Program_Version
                                         }

-- | ID tag for @"SAM_V1_6_Program"@.
data SAM_V1_6_Program_Record_Identifier = SAM_V1_6_Program_Record_Identifier { sam_v1_6_program_record_identifier_tag   :: Seq Word8
                                                                             , sam_v1_6_program_record_identifier_value :: ByteString
                                                                             }

-- | PN tag for @"SAM_V1_6_Program"@.
data SAM_V1_6_Program_Name = SAM_V1_6_Program_Name { sam_v1_6_program_name_tag   :: Seq Word8
                                                   , sam_v1_6_program_name_value :: ByteString
                                                   }

-- | CL tag for @"SAM_V1_6_Program"@.
data SAM_V1_6_Program_Command_Line = SAM_V1_6_Program_Command_Line { sam_v1_6_program_command_line_tag   :: Seq Word8
                                                                   , sam_v1_6_program_command_line_value :: ByteString
                                                                   }

-- | PP tag for @"SAM_V1_6_Program"@.
data SAM_V1_6_Program_Previous_PG_ID = SAM_V1_6_Program_Previous_PG_ID { sam_v1_6_program_previous_pg_id_tag   :: Seq Word8
                                                                       , sam_v1_6_program_previous_pg_id_value :: ByteString
                                                                       }

-- | DS tag for @"SAM_V1_6_Program"@.
data SAM_V1_6_Program_Description = SAM_V1_6_Program_Description { sam_v1_6_program_description_tag   :: Seq Word8
                                                                 , sam_v1_6_program_description_value :: ByteString
                                                                 }

-- | VN tag for @"SAM_V1_6_Program"@.
data SAM_V1_6_Program_Version = SAM_V1_6_Program_Version { sam_v1_6_program_version_tag   :: Seq Word8
                                                         , sam_v1_6_program_version_value :: ByteString
                                                         }