hs-samtools-0.3.0.0: Read and write SAM, BAM, and CRAM files.
Copyright(c) Matthew Mosior 2023
LicenseBSD-style
Maintainermattm.github@gmail.com
Portabilityportable
Safe HaskellSafe-Inferred
LanguageHaskell2010

Data.SAM.Version1_6.Alignment.Base

Description

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 library for the above warning text.

Description

This library enables the decoding/encoding of SAM, BAM and CRAM file formats.

Synopsis

SAM version 1.6 alignment mandatory and optional data types

data SAM_V1_6_Alignment Source #

Custom SAM (version 1.6) SAM_V1_6_Alignment data type. See section 1.4 and 1.5 of the SAM v1.6 specification documentation.

Instances

Instances details
Generic SAM_V1_6_Alignment Source # 
Instance details

Defined in Data.SAM.Version1_6.Alignment.Base

Associated Types

type Rep SAM_V1_6_Alignment :: Type -> Type #

Show SAM_V1_6_Alignment Source # 
Instance details

Defined in Data.SAM.Version1_6.Alignment.Base

type Rep SAM_V1_6_Alignment Source # 
Instance details

Defined in Data.SAM.Version1_6.Alignment.Base

type Rep SAM_V1_6_Alignment = D1 ('MetaData "SAM_V1_6_Alignment" "Data.SAM.Version1_6.Alignment.Base" "hs-samtools-0.3.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Alignment" 'PrefixI 'True) ((((S1 ('MetaSel ('Just "sam_v1_6_alignment_qname") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_flag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int)) :*: (S1 ('MetaSel ('Just "sam_v1_6_alignment_rname") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_pos") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Integer))) :*: ((S1 ('MetaSel ('Just "sam_v1_6_alignment_mapq") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Int) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_cigar") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)) :*: (S1 ('MetaSel ('Just "sam_v1_6_alignment_rnext") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_pnext") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Integer)))) :*: (((S1 ('MetaSel ('Just "sam_v1_6_alignment_tlen") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 Integer) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_seq") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)) :*: (S1 ('MetaSel ('Just "sam_v1_6_alignment_qual") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_aopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe ByteString)))) :*: ((S1 ('MetaSel ('Just "sam_v1_6_alignment_iopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Integer)) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_fopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe Float))) :*: (S1 ('MetaSel ('Just "sam_v1_6_alignment_zopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe ByteString)) :*: (S1 ('MetaSel ('Just "sam_v1_6_alignment_hopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (Seq Word8))) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment_bopt") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Alignment_BOPT))))))))