Copyright | (c) Matthew Mosior 2024 |
---|---|
License | BSD-style |
Maintainer | mattm.github@gmail.com |
Portability | portable |
Safe Haskell | Safe-Inferred |
Language | Haskell2010 |
Data.SAM.Version1_6.Header.SQ
Description
Description
This library enables the decoding/encoding of SAM, BAM and CRAM file formats.
Synopsis
- data SAM_V1_6_Reference_Sequence_Dictionary = SAM_V1_6_Reference_Sequence_Dictionary {
- sam_v1_6_reference_sequence_dictionary_reference_sequence_name :: SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name
- sam_v1_6_reference_sequence_dictionary_reference_sequence_length :: SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length
- sam_v1_6_reference_sequence_dictionary_alternative_locus :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus
- sam_v1_6_reference_sequence_dictionary_alternative_reference_sequence_names :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names
- sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier
- sam_v1_6_reference_sequence_dictionary_description :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description
- sam_v1_6_reference_sequence_dictionary_md5_checksum :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum
- sam_v1_6_reference_sequence_dictionary_species :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species
- sam_v1_6_reference_sequence_dictionary_molecule_topology :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology
- sam_v1_6_reference_sequence_dictionary_uri :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI
- newtype SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name {}
- newtype SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length {}
- newtype SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus = SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus {}
- newtype SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names = SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names {}
- newtype SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier = SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier {}
- newtype SAM_V1_6_Reference_Sequence_Dictionary_Description = SAM_V1_6_Reference_Sequence_Dictionary_Description {}
- newtype SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum = SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum {}
- newtype SAM_V1_6_Reference_Sequence_Dictionary_Species = SAM_V1_6_Reference_Sequence_Dictionary_Species {}
- newtype SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology = SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology {}
- newtype SAM_V1_6_Reference_Sequence_Dictionary_URI = SAM_V1_6_Reference_Sequence_Dictionary_URI {}
SAM version 1.6 Reference sequence dictionary data type
data SAM_V1_6_Reference_Sequence_Dictionary Source #
Custom SAM (version 1.6) SAM_V1_6_Reference_Sequence_Dictionary
data type.
See section 1.3 of the SAM v1.6 specification documentation.
Constructors
Instances
SAM version 1.6 Reference sequence dictionary data types
newtype SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name Source #
SN tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
newtype SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length Source #
LN tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
newtype SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus Source #
AH tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
Generic SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus Source # | |
Defined in Data.SAM.Version1_6.Header.SQ Associated Types type Rep SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus :: Type -> Type # | |
Show SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus Source # | |
Eq SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus Source # | |
Defined in Data.SAM.Version1_6.Header.SQ | |
type Rep SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus Source # | |
Defined in Data.SAM.Version1_6.Header.SQ type Rep SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus = D1 ('MetaData "SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus" "Data.SAM.Version1_6.Header.SQ" "hs-samtools-0.10.0.2-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_alternative_locus_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names Source #
AN tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
newtype SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier Source #
AS tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
newtype SAM_V1_6_Reference_Sequence_Dictionary_Description Source #
DS tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
Generic SAM_V1_6_Reference_Sequence_Dictionary_Description Source # | |
Defined in Data.SAM.Version1_6.Header.SQ Associated Types type Rep SAM_V1_6_Reference_Sequence_Dictionary_Description :: Type -> Type # | |
Show SAM_V1_6_Reference_Sequence_Dictionary_Description Source # | |
Eq SAM_V1_6_Reference_Sequence_Dictionary_Description Source # | |
type Rep SAM_V1_6_Reference_Sequence_Dictionary_Description Source # | |
Defined in Data.SAM.Version1_6.Header.SQ type Rep SAM_V1_6_Reference_Sequence_Dictionary_Description = D1 ('MetaData "SAM_V1_6_Reference_Sequence_Dictionary_Description" "Data.SAM.Version1_6.Header.SQ" "hs-samtools-0.10.0.2-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_Description" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_description_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum Source #
M5 tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
Generic SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum Source # | |
Defined in Data.SAM.Version1_6.Header.SQ Associated Types type Rep SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum :: Type -> Type # | |
Show SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum Source # | |
Eq SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum Source # | |
type Rep SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum Source # | |
Defined in Data.SAM.Version1_6.Header.SQ type Rep SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum = D1 ('MetaData "SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum" "Data.SAM.Version1_6.Header.SQ" "hs-samtools-0.10.0.2-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_md5_checksum_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Reference_Sequence_Dictionary_Species Source #
SP tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Constructors
SAM_V1_6_Reference_Sequence_Dictionary_Species | |
Instances
Generic SAM_V1_6_Reference_Sequence_Dictionary_Species Source # | |
Defined in Data.SAM.Version1_6.Header.SQ Associated Types type Rep SAM_V1_6_Reference_Sequence_Dictionary_Species :: Type -> Type # | |
Show SAM_V1_6_Reference_Sequence_Dictionary_Species Source # | |
Eq SAM_V1_6_Reference_Sequence_Dictionary_Species Source # | |
type Rep SAM_V1_6_Reference_Sequence_Dictionary_Species Source # | |
Defined in Data.SAM.Version1_6.Header.SQ type Rep SAM_V1_6_Reference_Sequence_Dictionary_Species = D1 ('MetaData "SAM_V1_6_Reference_Sequence_Dictionary_Species" "Data.SAM.Version1_6.Header.SQ" "hs-samtools-0.10.0.2-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_Species" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_species_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology Source #
TP tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
Generic SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology Source # | |
Defined in Data.SAM.Version1_6.Header.SQ Associated Types type Rep SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology :: Type -> Type # | |
Show SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology Source # | |
Eq SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology Source # | |
Defined in Data.SAM.Version1_6.Header.SQ | |
type Rep SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology Source # | |
Defined in Data.SAM.Version1_6.Header.SQ type Rep SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology = D1 ('MetaData "SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology" "Data.SAM.Version1_6.Header.SQ" "hs-samtools-0.10.0.2-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_molecule_topology_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
newtype SAM_V1_6_Reference_Sequence_Dictionary_URI Source #
UR tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Constructors
SAM_V1_6_Reference_Sequence_Dictionary_URI | |
Instances
Generic SAM_V1_6_Reference_Sequence_Dictionary_URI Source # | |
Defined in Data.SAM.Version1_6.Header.SQ Associated Types type Rep SAM_V1_6_Reference_Sequence_Dictionary_URI :: Type -> Type # | |
Show SAM_V1_6_Reference_Sequence_Dictionary_URI Source # | |
Defined in Data.SAM.Version1_6.Header.SQ | |
Eq SAM_V1_6_Reference_Sequence_Dictionary_URI Source # | |
type Rep SAM_V1_6_Reference_Sequence_Dictionary_URI Source # | |
Defined in Data.SAM.Version1_6.Header.SQ type Rep SAM_V1_6_Reference_Sequence_Dictionary_URI = D1 ('MetaData "SAM_V1_6_Reference_Sequence_Dictionary_URI" "Data.SAM.Version1_6.Header.SQ" "hs-samtools-0.10.0.2-inplace" 'True) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_URI" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_uri_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |