hs-samtools-0.5.0.2: src/Data/SAM/Version1_6/Alignment/Base.hs
{-# 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
--
-- = 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_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_flag :: Int -- ^ Combination of bitwise FLAGs.
, 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_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_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_cigar :: ByteString -- ^ CIGAR string (set ‘*’ if unavailable).
, 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_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_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_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_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_aopt :: Maybe ByteString -- ^ A - [!-~] - Printable characters.
, sam_v1_6_alignment_iopt :: Maybe Integer -- ^ i - [-+]?[0-9]+ - Signed integer.
, sam_v1_6_alignment_fopt :: Maybe Float -- ^ f - [-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)? - Single-precision floating number.
, sam_v1_6_alignment_zopt :: Maybe ByteString -- ^ Z - [ !-~]* - Printable string, including space.
, 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_bopt :: Maybe SAM_V1_6_Alignment_BOPT -- ^ B - [cCsSiIf]​(,[-+]?[0-9]*\.?[0-9]+([eE][-+]?[0-9]+)?)* - Integer or numeric array.
}
deriving (Generic,Typeable)
instance Show SAM_V1_6_Alignment where
show (SAM_V1_6_Alignment qname flag rname pos mapq cigar rnext pnext tlen seq qual aopt iopt fopt zopt hopt bopt) =
"SAM_V1_6_Alignment { " ++
"qname = " ++
(show qname) ++
" , flag = " ++
(show flag) ++
" , rname = " ++
(show rname) ++
" , pos = " ++
(show pos) ++
" , mapq = " ++
(show mapq) ++
" , cigar = " ++
(show cigar) ++
" , rnext = " ++
(show rnext) ++
" , pnext = " ++
(show pnext) ++
" , tlen = " ++
(show tlen) ++
" , seq = " ++
(show seq) ++
" , qual = " ++
(show qual) ++
" , aopt = " ++
( show aopt) ++
" , iopt = " ++
(show iopt) ++
" , fopt = " ++
(show fopt) ++
" , zopt = " ++
(show zopt) ++
" , hopt = " ++
(show hopt) ++
" , bopt = " ++
(show bopt) ++
" }"