Copyright | (c) Matthew Mosior 2023 |
---|---|
License | BSD-style |
Maintainer | mattm.github@gmail.com |
Portability | portable |
Safe Haskell | Safe-Inferred |
Language | Haskell2010 |
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
- 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_reference_alternative_locus :: Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus
- sam_v1_6_reference_sequence_dictionary_reference_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
- data SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name {}
- data SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length = SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length {}
- data SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus = SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus {}
- data SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names = SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names {}
- data SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier = SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier {}
- data SAM_V1_6_Reference_Sequence_Dictionary_Description = SAM_V1_6_Reference_Sequence_Dictionary_Description {}
- data SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum = SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum {}
- data SAM_V1_6_Reference_Sequence_Dictionary_Species = SAM_V1_6_Reference_Sequence_Dictionary_Species {}
- data SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology = SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology {}
- data 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.
Instances
SAM version 1.6 Reference sequence dictionary data types
data SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name Source #
SN tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
data SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length Source #
LN tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
data SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus Source #
AH tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
data SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names Source #
AN tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
data SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier Source #
AS tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
data 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 | |
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-0.4.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_Description" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_description_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_description_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data 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 | |
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-0.4.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_md5_checksum_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_md5_checksum_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data SAM_V1_6_Reference_Sequence_Dictionary_Species Source #
SP tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
Generic 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 :: 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-0.4.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_Species" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_species_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_species_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |
data SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology Source #
TP tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
data SAM_V1_6_Reference_Sequence_Dictionary_URI Source #
UR tag for SAM_V1_6_Reference_Sequence_Dictionary
.
Instances
Generic 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 :: Type -> Type # | |
Show SAM_V1_6_Reference_Sequence_Dictionary_URI Source # | |
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-0.4.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_URI" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_uri_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_uri_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString))) |