Copyright	(c) Matthew Mosior 2023
License	BSD-style
Maintainer	mattm.github@gmail.com
Portability	portable
Safe Haskell	Safe-Inferred
Language	Haskell2010

Data.SAM.Version1_6.Base

Contents

SAM version 1.6 data type

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.

SAM version 1.6 data type

data SAM_V1_6 Source #

Custom SAM_V1_6 (SAM version 1.6) data type. See the SAM v1.6 specification documentation.

Constructors

SAM_V1_6

Fields

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_reference_sequence_dictionary :: Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary)
Reference sequence dictionary. The order of @SQ lines defines the alignment sorting order.
sam_v1_6_read_group :: Maybe (Seq SAM_V1_6_Read_Group)
Read group. Unordered multiple @RG lines are allowed.
sam_v1_6_program :: Maybe SAM_V1_6_Program
Program.
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_alignment :: Seq SAM_V1_6_Alignment
The alignment section (mandatory and optional fields).

Instances

Instances details

Generic SAM_V1_6 Source #
Instance details Defined in Data.SAM.Version1_6.Base Associated Types type Rep SAM_V1_6 :: Type -> Type # Methods from :: SAM_V1_6 -> Rep SAM_V1_6 x # to :: Rep SAM_V1_6 x -> SAM_V1_6 #
Show SAM_V1_6 Source #
Instance details Defined in Data.SAM.Version1_6.Base Methods showsPrec :: Int -> SAM_V1_6 -> ShowS # show :: SAM_V1_6 -> String # showList :: [SAM_V1_6] -> ShowS #
type Rep SAM_V1_6 Source #
Instance details Defined in Data.SAM.Version1_6.Base type Rep SAM_V1_6 = D1 ('MetaData "SAM_V1_6" "Data.SAM.Version1_6.Base" "hs-samtools-0.5.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6" 'PrefixI 'True) ((S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_File_Level_Metadata)) :: (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (Seq SAM_V1_6_Reference_Sequence_Dictionary))) :: S1 ('MetaSel ('Just "sam_v1_6_read_group") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (Seq SAM_V1_6_Read_Group))))) :: (S1 ('MetaSel ('Just "sam_v1_6_program") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Program)) :: (S1 ('MetaSel ('Just "sam_v1_6_one_line_comment") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe (Seq SAM_V1_6_One_Line_Comment))) :*: S1 ('MetaSel ('Just "sam_v1_6_alignment") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq SAM_V1_6_Alignment))))))