{-# LANGUAGE DeriveDataTypeable          #-}
{-# LANGUAGE DeriveGeneric               #-}
{-# LANGUAGE FlexibleContexts            #-}
{-# LANGUAGE FlexibleInstances           #-}
{-# LANGUAGE MultiParamTypeClasses       #-}
{-# LANGUAGE OverloadedLists             #-}
{-# LANGUAGE OverloadedStrings           #-}
{-# LANGUAGE PackageImports              #-}
{-# LANGUAGE RecordWildCards             #-}
{-# LANGUAGE TemplateHaskell             #-}
{-# LANGUAGE TypeFamilies                #-}
{-# Language QuasiQuotes                 #-}
{-# OPTIONS_GHC -fno-warn-name-shadowing #-}

-- |
-- Module      :  Data.SAM.Version1_6.Alignment.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.Alignment.Base ( -- * SAM version 1.6 alignment mandatory and optional data types
                                            SAM_V1_6_Alignment(..)
                                          ) where

import Data.SAM.Version1_6.Alignment.BOPT

import Data.ByteString
import Data.Data
import Data.Sequence
import Data.Word
import Generics.Deriving.Base

-- | Custom SAM (version 1.6) @"SAM_V1_6_Alignment"@ data type.
-- See section 1.4 and 1.5 of the [SAM v1.6](http://samtools.github.io/hts-specs/SAMv1.pdf) specification documentation.
data SAM_V1_6_Alignment = SAM_V1_6_Alignment { SAM_V1_6_Alignment -> ByteString
sam_v1_6_alignment_qname :: ByteString                    -- ^ Query template NAME.
                                                                                                         -- reads/segments having identical QNAME are regarded to come from
                                                                                                         -- the same template. A QNAME ‘*’ indicates the information
                                                                                                         -- is unavailable. In a SAM file, a read may
                                                                                                         -- occupy multiple alignment lines, when its alignment is chimeric
                                                                                                         -- or when multiple mappings are given.
                                             , SAM_V1_6_Alignment -> Int
sam_v1_6_alignment_flag  :: Int                           -- ^ Combination of bitwise FLAGs.
                                             , SAM_V1_6_Alignment -> ByteString
sam_v1_6_alignment_rname :: ByteString                    -- ^ Reference sequence NAME of the alignment.
                                                                                                         -- If @SQ header lines are present, RNAME (if not
                                                                                                         -- ‘*’) must be present in one of the SQ-SN tag.
                                                                                                         -- An unmapped segment without coordinate has a ‘*’ at
                                                                                                         -- this field. However, an unmapped segment may also have
                                                                                                         -- an ordinary coordinate such that it can be
                                                                                                         -- placed at a desired position after sorting.
                                                                                                         -- If RNAME is ‘*’, no assumptions can be made about POS
                                                                                                         -- and CIGAR.
                                             , SAM_V1_6_Alignment -> Integer
sam_v1_6_alignment_pos   :: Integer                       -- ^ 1-based leftmost mapping POSition of the first CIGAR
                                                                                                         -- operation that “consumes” a reference
                                                                                                         -- base. The first base in a reference sequence has coordinate 1.
                                                                                                         -- POS is set as 0 for an unmapped read without coordinate.
                                                                                                         -- If POS is 0, no assumptions can be made about RNAME and CIGAR.
                                             , SAM_V1_6_Alignment -> Int
sam_v1_6_alignment_mapq  :: Int                           -- ^ MAPping Quality. It equals −10 log10 Pr{mapping position is wrong},
                                                                                                         -- rounded to the nearest integer. A value 255 indicates that the
                                                                                                         -- mapping quality is not available.
                                             , SAM_V1_6_Alignment -> ByteString
sam_v1_6_alignment_cigar :: ByteString                    -- ^ CIGAR string (set ‘*’ if unavailable).
                                             , SAM_V1_6_Alignment -> ByteString
sam_v1_6_alignment_rnext :: ByteString                    -- ^ Reference sequence name of the primary alignment of the
                                                                                                         -- NEXT read in the template. For the last read, the next read
                                                                                                         -- is the first read in the template. If @SQ header lines are present,
                                                                                                         -- RNEXT (if not ‘*’ or ‘=’) must be present in one of the SQ-SN tag.
                                                                                                         -- This field is set as ‘*’ when the information is unavailable,
                                                                                                         -- and set as ‘=’ if RNEXT is identical RNAME. If not ‘=’ and the next
                                                                                                         -- read in the template has one primary mapping (see also bit 0x100 in FLAG),
                                                                                                         -- this field is identical to RNAME at the primary line of the next read.
                                                                                                         -- If RNEXT is ‘*’, no assumptions can be made on PNEXT and bit 0x20.
                                             , SAM_V1_6_Alignment -> Integer
sam_v1_6_alignment_pnext :: Integer                       -- ^ 1-based Position of the primary alignment of the NEXT read in
                                                                                                         -- the template. Set as 0 when the information is unavailable.
                                                                                                         -- This field equals POS at the primary line of the next read.
                                                                                                         -- If PNEXT is 0, no assumptions can be made on RNEXT and bit 0x20.
                                             , SAM_V1_6_Alignment -> Integer
sam_v1_6_alignment_tlen  :: Integer                       -- ^ signed observed Template LENgth. For primary reads where the primary
                                                                                                         -- alignments of all reads in the template are mapped to the same reference
                                                                                                         -- sequence, the absolute value of TLEN equals the distance between the
                                                                                                         -- mapped end of the template and the mapped start of the template,
                                                                                                         -- inclusively (i.e., end − start + 1).
                                                                                                         -- Note that mapped base is defined to be one that aligns to the
                                                                                                         -- reference as described by CIGAR, hence excludes soft-clipped bases.
                                                                                                         -- The TLEN field is positive for the leftmost segment of the template,
                                                                                                         -- negative for the rightmost, and the sign for any middle segment is undefined.
                                                                                                         -- If segments cover the same coordinates then the choice of which is leftmost
                                                                                                         -- and rightmost is arbitrary, but the two ends must still have differing signs.
                                                                                                         -- It is set as 0 for a single-segment template or when the information
                                                                                                         -- is unavailable (e.g., when the first or last segment of a multi-segment
                                                                                                         -- template is unmapped or when the two are mapped to
                                                                                                         -- different reference sequences).
                                             , SAM_V1_6_Alignment -> ByteString
sam_v1_6_alignment_seq   :: ByteString                    -- ^ segment SEQuence. This field can be a ‘*’ when the sequence
                                                                                                         -- is not stored. If not a ‘*’, the length of the sequence must
                                                                                                         -- equal the sum of lengths of M/I/S/=/X operations in CIGAR.
                                                                                                         -- An ‘=’ denotes the base is identical to the reference base.
                                                                                                         -- No assumptions can be made on the letter cases.
                                             , SAM_V1_6_Alignment -> ByteString
sam_v1_6_alignment_qual  :: ByteString                    -- ^ ASCII of base QUALity plus 33 (same as the quality string
                                                                                                         -- in the Sanger FASTQ format). A base quality is the phred-scaled
                                                                                                         -- base error probability which equals −10 log10 Pr{base is wrong}.
                                                                                                         -- This field can be a ‘*’ when quality is not stored.
                                                                                                         -- If not a ‘*’, SEQ must not be a ‘*’ and the length of the quality
                                                                                                         -- string ought to equal the length of SEQ.
                                             , SAM_V1_6_Alignment -> Maybe ByteString
sam_v1_6_alignment_aopt  :: Maybe ByteString              -- ^ A - [!-~] - Printable characters.
                                             , SAM_V1_6_Alignment -> Maybe Integer
sam_v1_6_alignment_iopt  :: Maybe Integer                 -- ^ i - [-+]?[0-9]+ - Signed integer.
                                             , SAM_V1_6_Alignment -> Maybe Float
sam_v1_6_alignment_fopt  :: Maybe Float                   -- ^ f - [-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? - Single-precision floating number.
                                             , SAM_V1_6_Alignment -> Maybe ByteString
sam_v1_6_alignment_zopt  :: Maybe ByteString              -- ^ Z - [ !-~]* - Printable string, including space.
                                             , SAM_V1_6_Alignment -> Maybe (Seq Word8)
sam_v1_6_alignment_hopt  :: Maybe (Seq Word8)             -- ^ H - ([0-9A-F][0-9A-F])* - Byte array in the Hex format.
                                             , SAM_V1_6_Alignment -> Maybe SAM_V1_6_Alignment_BOPT
sam_v1_6_alignment_bopt  :: Maybe SAM_V1_6_Alignment_BOPT -- ^ B - [cCsSiIf]​(,[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* - Integer or numeric array.
                                             }
  deriving ((forall x. SAM_V1_6_Alignment -> Rep SAM_V1_6_Alignment x)
-> (forall x. Rep SAM_V1_6_Alignment x -> SAM_V1_6_Alignment)
-> Generic SAM_V1_6_Alignment
forall x. Rep SAM_V1_6_Alignment x -> SAM_V1_6_Alignment
forall x. SAM_V1_6_Alignment -> Rep SAM_V1_6_Alignment x
forall a.
(forall x. a -> Rep a x) -> (forall x. Rep a x -> a) -> Generic a
$cfrom :: forall x. SAM_V1_6_Alignment -> Rep SAM_V1_6_Alignment x
from :: forall x. SAM_V1_6_Alignment -> Rep SAM_V1_6_Alignment x
$cto :: forall x. Rep SAM_V1_6_Alignment x -> SAM_V1_6_Alignment
to :: forall x. Rep SAM_V1_6_Alignment x -> SAM_V1_6_Alignment
Generic,Typeable)

instance Show SAM_V1_6_Alignment where
  show :: SAM_V1_6_Alignment -> String
show (SAM_V1_6_Alignment ByteString
qname Int
flag ByteString
rname Integer
pos Int
mapq ByteString
cigar ByteString
rnext Integer
pnext Integer
tlen ByteString
seq ByteString
qual Maybe ByteString
aopt Maybe Integer
iopt Maybe Float
fopt Maybe ByteString
zopt Maybe (Seq Word8)
hopt Maybe SAM_V1_6_Alignment_BOPT
bopt) =
    String
"SAM_V1_6_Alignment { " String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
"qname = "              String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (ByteString -> String
forall a. Show a => a -> String
show ByteString
qname)            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , flag = "            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Int -> String
forall a. Show a => a -> String
show Int
flag)             String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , rname = "           String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (ByteString -> String
forall a. Show a => a -> String
show ByteString
rname)            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , pos = "             String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Integer -> String
forall a. Show a => a -> String
show Integer
pos)              String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , mapq = "            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Int -> String
forall a. Show a => a -> String
show Int
mapq)             String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , cigar = "           String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (ByteString -> String
forall a. Show a => a -> String
show ByteString
cigar)            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , rnext = "           String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (ByteString -> String
forall a. Show a => a -> String
show ByteString
rnext)            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , pnext = "           String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Integer -> String
forall a. Show a => a -> String
show Integer
pnext)            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , tlen = "            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Integer -> String
forall a. Show a => a -> String
show Integer
tlen)             String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , seq = "             String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (ByteString -> String
forall a. Show a => a -> String
show ByteString
seq)              String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , qual = "            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (ByteString -> String
forall a. Show a => a -> String
show ByteString
qual)             String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , aopt = "            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    ( Maybe ByteString -> String
forall a. Show a => a -> String
show Maybe ByteString
aopt)            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , iopt = "            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Maybe Integer -> String
forall a. Show a => a -> String
show Maybe Integer
iopt)             String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , fopt = "            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Maybe Float -> String
forall a. Show a => a -> String
show Maybe Float
fopt)             String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , zopt = "            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Maybe ByteString -> String
forall a. Show a => a -> String
show Maybe ByteString
zopt)             String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , hopt = "            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Maybe (Seq Word8) -> String
forall a. Show a => a -> String
show Maybe (Seq Word8)
hopt)             String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" , bopt = "            String -> ShowS
forall a. [a] -> [a] -> [a]
++
    (Maybe SAM_V1_6_Alignment_BOPT -> String
forall a. Show a => a -> String
show Maybe SAM_V1_6_Alignment_BOPT
bopt)             String -> ShowS
forall a. [a] -> [a] -> [a]
++
    String
" }"