{-# 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.Base
-- 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.Base ( -- * SAM version 1.6 data type
                                  SAM_V1_6(..)
                                ) where

import Data.SAM.Version1_6.Alignment
import Data.SAM.Version1_6.Header

import Data.Data
import Data.Sequence
import Generics.Deriving.Base

-- | Custom @"SAM_V1_6"@ (SAM version 1.6) data type.
-- See the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.
data SAM_V1_6 = SAM_V1_6 { SAM_V1_6 -> Maybe SAM_V1_6_File_Level_Metadata
sam_v1_6_file_level_metadata           :: Maybe SAM_V1_6_File_Level_Metadata           -- ^ File-level metadata.
                                                                                                                  -- Optional. If present,
                                                                                                                  -- there must be only one
                                                                                                                  -- @HD line and it must be
                                                                                                                  -- the first line of the file. 
                         , SAM_V1_6 -> Maybe SAM_V1_6_Reference_Sequence_Dictionary
sam_v1_6_reference_sequence_dictionary :: Maybe SAM_V1_6_Reference_Sequence_Dictionary -- ^ Reference sequence dictionary.
                                                                                                                  -- The order of @SQ lines defines the
                                                                                                                  -- alignment sorting order.
                         , SAM_V1_6 -> Maybe (Seq SAM_V1_6_Read_Group)
sam_v1_6_read_group                    :: Maybe (Seq SAM_V1_6_Read_Group)              -- ^ Read group.
                                                                                                                  -- Unordered multiple @RG
                                                                                                                  -- lines are allowed.
                         , SAM_V1_6 -> Maybe SAM_V1_6_Program
sam_v1_6_program                       :: Maybe SAM_V1_6_Program                       -- ^ Program.
                         , SAM_V1_6 -> Maybe (Seq SAM_V1_6_One_Line_Comment)
sam_v1_6_one_line_comment              :: Maybe (Seq SAM_V1_6_One_Line_Comment)        -- ^ One-line text comment.
                                                                                                                  -- Unordered multiple @CO lines
                                                                                                                  -- are allowed. UTF-8 encoding
                                                                                                                  -- may be used.
                         , SAM_V1_6 -> Seq SAM_V1_6_Alignment
sam_v1_6_alignment                     :: Seq SAM_V1_6_Alignment                       -- ^ The alignment section (mandatory
                                                                                                                  -- and optional fields).
                         }
  deriving ((forall x. SAM_V1_6 -> Rep SAM_V1_6 x)
-> (forall x. Rep SAM_V1_6 x -> SAM_V1_6) -> Generic SAM_V1_6
forall x. Rep SAM_V1_6 x -> SAM_V1_6
forall x. SAM_V1_6 -> Rep SAM_V1_6 x
forall a.
(forall x. a -> Rep a x) -> (forall x. Rep a x -> a) -> Generic a
$cfrom :: forall x. SAM_V1_6 -> Rep SAM_V1_6 x
from :: forall x. SAM_V1_6 -> Rep SAM_V1_6 x
$cto :: forall x. Rep SAM_V1_6 x -> SAM_V1_6
to :: forall x. Rep SAM_V1_6 x -> SAM_V1_6
Generic,Typeable)

instance Show SAM_V1_6 where
  show :: SAM_V1_6 -> String
show (SAM_V1_6 Maybe SAM_V1_6_File_Level_Metadata
file_level_metadata
                 Maybe SAM_V1_6_Reference_Sequence_Dictionary
reference_sequence_dictionary
                 Maybe (Seq SAM_V1_6_Read_Group)
read_group Maybe SAM_V1_6_Program
program
                 Maybe (Seq SAM_V1_6_One_Line_Comment)
one_line_comment
                 Seq SAM_V1_6_Alignment
alignment
       ) =
    String
"SAM_V1_6 { "                         String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
"file_level_metadata = "              String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Maybe SAM_V1_6_File_Level_Metadata -> String
forall a. Show a => a -> String
show Maybe SAM_V1_6_File_Level_Metadata
file_level_metadata)            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , reference_sequence_dictionary = " String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Maybe SAM_V1_6_Reference_Sequence_Dictionary -> String
forall a. Show a => a -> String
show Maybe SAM_V1_6_Reference_Sequence_Dictionary
reference_sequence_dictionary)  String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , read_group = "                    String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Maybe (Seq SAM_V1_6_Read_Group) -> String
forall a. Show a => a -> String
show Maybe (Seq SAM_V1_6_Read_Group)
read_group)                     String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , program = "                       String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Maybe SAM_V1_6_Program -> String
forall a. Show a => a -> String
show Maybe SAM_V1_6_Program
program)                        String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , one_line_comment = "              String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Maybe (Seq SAM_V1_6_One_Line_Comment) -> String
forall a. Show a => a -> String
show Maybe (Seq SAM_V1_6_One_Line_Comment)
one_line_comment)               String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , alignment = "                     String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Seq SAM_V1_6_Alignment -> String
forall a. Show a => a -> String
show Seq SAM_V1_6_Alignment
alignment)                      String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" }"