Copyright | (c) Matthew Mosior 2023 |
---|---|
License | BSD-style |
Maintainer | mattm.github@gmail.com |
Portability | portable |
Safe Haskell | Safe-Inferred |
Language | Haskell2010 |
Description
This library enables the decoding/encoding of SAM, BAM and CRAM file formats.
Synopsis
- data SAM_V1_6_File_Level_Metadata = SAM_V1_6_File_Level_Metadata {
- sam_v1_6_file_level_metadata_format_version :: SAM_V1_6_File_Level_Metadata_Format_Version
- sam_v1_6_file_level_metadata_sorting_order :: Maybe SAM_V1_6_File_Level_Metadata_Sorting_Order
- sam_v1_6_file_level_metadata_alignment_grouping :: Maybe SAM_V1_6_File_Level_Metadata_Alignment_Grouping
- sam_v1_6_file_level_metadata_subsorting_order :: Maybe SAM_V1_6_File_Level_Metadata_SubSorting_Order
- data SAM_V1_6_File_Level_Metadata_Format_Version = SAM_V1_6_File_Level_Metadata_Format_Version {}
- data SAM_V1_6_File_Level_Metadata_Sorting_Order = SAM_V1_6_File_Level_Metadata_Sorting_Order {}
- data SAM_V1_6_File_Level_Metadata_Alignment_Grouping = SAM_V1_6_File_Level_Metadata_Alignment_Grouping {}
- data SAM_V1_6_File_Level_Metadata_SubSorting_Order = SAM_V1_6_File_Level_Metadata_SubSorting_Order {}
SAM version 1.6 File-level metadata data type
data SAM_V1_6_File_Level_Metadata Source #
Custom SAM (version 1.6) SAM_V1_6_File_Level_Metadata
data type.
See section 1.3 of the SAM v1.6 specification documentation.
Instances
SAM version 1.6 File-Level Metadata data types
data SAM_V1_6_File_Level_Metadata_Format_Version Source #
VN tag for SAM_V1_6_File_Level_Metadata
.
Instances
Generic SAM_V1_6_File_Level_Metadata_Format_Version Source # | |
Defined in Data.SAM.Version1_6.Header.HD type Rep SAM_V1_6_File_Level_Metadata_Format_Version :: Type -> Type # | |
Show SAM_V1_6_File_Level_Metadata_Format_Version Source # | |
Eq SAM_V1_6_File_Level_Metadata_Format_Version Source # | |
type Rep SAM_V1_6_File_Level_Metadata_Format_Version Source # | |
Defined in Data.SAM.Version1_6.Header.HD type Rep SAM_V1_6_File_Level_Metadata_Format_Version = D1 ('MetaData "SAM_V1_6_File_Level_Metadata_Format_Version" "Data.SAM.Version1_6.Header.HD" "hs-samtools-0.5.0.2-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_File_Level_Metadata_Format_Version" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_format_version_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_format_version_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data SAM_V1_6_File_Level_Metadata_Sorting_Order Source #
SO tag for SAM_V1_6_File_Level_Metadata
.
Instances
Generic SAM_V1_6_File_Level_Metadata_Sorting_Order Source # | |
Defined in Data.SAM.Version1_6.Header.HD type Rep SAM_V1_6_File_Level_Metadata_Sorting_Order :: Type -> Type # | |
Show SAM_V1_6_File_Level_Metadata_Sorting_Order Source # | |
Eq SAM_V1_6_File_Level_Metadata_Sorting_Order Source # | |
type Rep SAM_V1_6_File_Level_Metadata_Sorting_Order Source # | |
Defined in Data.SAM.Version1_6.Header.HD type Rep SAM_V1_6_File_Level_Metadata_Sorting_Order = D1 ('MetaData "SAM_V1_6_File_Level_Metadata_Sorting_Order" "Data.SAM.Version1_6.Header.HD" "hs-samtools-0.5.0.2-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_File_Level_Metadata_Sorting_Order" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_sorting_order_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_sorting_order_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data SAM_V1_6_File_Level_Metadata_Alignment_Grouping Source #
GO tag for SAM_V1_6_File_Level_Metadata
.
Instances
Generic SAM_V1_6_File_Level_Metadata_Alignment_Grouping Source # | |
Defined in Data.SAM.Version1_6.Header.HD type Rep SAM_V1_6_File_Level_Metadata_Alignment_Grouping :: Type -> Type # | |
Show SAM_V1_6_File_Level_Metadata_Alignment_Grouping Source # | |
Eq SAM_V1_6_File_Level_Metadata_Alignment_Grouping Source # | |
type Rep SAM_V1_6_File_Level_Metadata_Alignment_Grouping Source # | |
Defined in Data.SAM.Version1_6.Header.HD type Rep SAM_V1_6_File_Level_Metadata_Alignment_Grouping = D1 ('MetaData "SAM_V1_6_File_Level_Metadata_Alignment_Grouping" "Data.SAM.Version1_6.Header.HD" "hs-samtools-0.5.0.2-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_File_Level_Metadata_Alignment_Grouping" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_alignment_grouping_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_alignment_grouping_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data SAM_V1_6_File_Level_Metadata_SubSorting_Order Source #
SS tag for SAM_V1_6_File_Level_Metadata
.
Instances
Generic SAM_V1_6_File_Level_Metadata_SubSorting_Order Source # | |
Defined in Data.SAM.Version1_6.Header.HD type Rep SAM_V1_6_File_Level_Metadata_SubSorting_Order :: Type -> Type # | |
Show SAM_V1_6_File_Level_Metadata_SubSorting_Order Source # | |
Eq SAM_V1_6_File_Level_Metadata_SubSorting_Order Source # | |
type Rep SAM_V1_6_File_Level_Metadata_SubSorting_Order Source # | |
Defined in Data.SAM.Version1_6.Header.HD type Rep SAM_V1_6_File_Level_Metadata_SubSorting_Order = D1 ('MetaData "SAM_V1_6_File_Level_Metadata_SubSorting_Order" "Data.SAM.Version1_6.Header.HD" "hs-samtools-0.5.0.2-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_File_Level_Metadata_SubSorting_Order" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_subsorting_order_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_file_level_metadata_subsorting_order_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |