{-# 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.HD
-- 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.HD ( -- * SAM version 1.6 File-level metadata data type
                                       SAM_V1_6_File_Level_Metadata(..),
                                       -- * SAM version 1.6 File-Level Metadata data types
                                       SAM_V1_6_File_Level_Metadata_Format_Version(..),
                                       SAM_V1_6_File_Level_Metadata_Sorting_Order(..),
                                       SAM_V1_6_File_Level_Metadata_Alignment_Grouping(..),
                                       SAM_V1_6_File_Level_Metadata_SubSorting_Order(..)
                                     ) where

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


-- | Custom SAM (version 1.6) @"SAM_V1_6_File_Level_Metadata"@ 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_File_Level_Metadata = SAM_V1_6_File_Level_Metadata { sam_v1_6_file_level_metadata_format_version     :: SAM_V1_6_File_Level_Metadata_Format_Version
                                                                 , sam_v1_6_file_level_metadata_sorting_order      :: Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order
                                                                 , sam_v1_6_file_level_metadata_alignment_grouping :: Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping
                                                                 , sam_v1_6_file_level_metadata_subsorting_order   :: Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order
                                                                 }

-- | VN tag for @"SAM_V1_6_File_Level_Metadata"@.
data SAM_V1_6_File_Level_Metadata_Format_Version = SAM_V1_6_File_Level_Metadata_Format_Version { sam_v1_6_file_level_metadata_format_version_tag   :: Seq Word8
                                                                                               , sam_v1_6_file_level_metadata_format_version_value :: ByteString
                                                                                               }

-- | SO tag for @"SAM_V1_6_File_Level_Metadata"@.
data SAM_V1_6_File_Level_Metadata_Sorting_Order = SAM_V1_6_File_Level_Metadata_Sorting_Order { sam_v1_6_file_level_metadata_sorting_order_tag   :: Seq Word8
                                                                                             , sam_v1_6_file_level_metadata_sorting_order_value :: ByteString
                                                                                             }

-- | GO tag for @"SAM_V1_6_File_Level_Metadata"@.
data SAM_V1_6_File_Level_Metadata_Alignment_Grouping = SAM_V1_6_File_Level_Metadata_Alignment_Grouping { sam_v1_6_file_level_metadata_alignment_grouping_tag   :: Seq Word8
                                                                                                       , sam_v1_6_file_level_metadata_alignment_grouping_value :: ByteString
                                                                                                       }

-- | SS tag for @"SAM_V1_6_File_Level_Metadata"@.
data SAM_V1_6_File_Level_Metadata_SubSorting_Order = SAM_V1_6_File_Level_Metadata_SubSorting_Order { sam_v1_6_file_level_metadata_subsorting_order_tag   :: Seq Word8
                                                                                                   , sam_v1_6_file_level_metadata_subsorting_order_value :: ByteString
                                                                                                   }