Data.SAM.Version1_6.Internal

Contents

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

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

Constructors

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 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.

Instances details

Generic SAM_V1_6 Source #
Instance details Defined in Data.SAM.Version1_6.Internal 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 #
type Rep SAM_V1_6 Source #
Instance details Defined in Data.SAM.Version1_6.Internal type Rep SAM_V1_6 = D1 ('MetaData "SAM_V1_6" "Data.SAM.Version1_6.Internal" "hs-samtools-0.2.0.0-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 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)))))))