hs-samtools-0.4.0.0: Read and write SAM, BAM, and CRAM files.
Copyright(c) Matthew Mosior 2023
LicenseBSD-style
Maintainermattm.github@gmail.com
Portabilityportable
Safe HaskellSafe-Inferred
LanguageHaskell2010

Data.SAM.Version1_6.Header.SQ

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

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.

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Generic SAM_V1_6_Reference_Sequence_Dictionary Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Show SAM_V1_6_Reference_Sequence_Dictionary Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary = D1 ('MetaData "SAM_V1_6_Reference_Sequence_Dictionary" "Data.SAM.Version1_6.Header.SQ" "hs-samtools-0.4.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary" 'PrefixI 'True) (((S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_reference_sequence_name") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name) :*: S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_reference_sequence_length") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length)) :*: (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_reference_alternative_locus") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus)) :*: (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_reference_alternative_reference_sequence_names") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names)) :*: S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier))))) :*: ((S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_description") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Description)) :*: S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_md5_checksum") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum))) :*: (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_species") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Species)) :*: (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_molecule_topology") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology)) :*: S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_uri") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Maybe SAM_V1_6_Reference_Sequence_Dictionary_URI)))))))

SAM version 1.6 Reference sequence dictionary data types

data SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name Source #

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Generic SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Show SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Eq SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name = D1 ('MetaData "SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name" "Data.SAM.Version1_6.Header.SQ" "hs-samtools-0.4.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

data SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length Source #

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Generic SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Show SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Eq SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length = D1 ('MetaData "SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length" "Data.SAM.Version1_6.Header.SQ" "hs-samtools-0.4.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

data SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus Source #

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Generic SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Show SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Eq SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus Source # 
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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-0.4.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_reference_alternative_locus_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_reference_alternative_locus_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

data SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names Source #

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Generic SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Show SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Eq SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names = D1 ('MetaData "SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names" "Data.SAM.Version1_6.Header.SQ" "hs-samtools-0.4.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_reference_alternative_reference_sequence_names_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_reference_alternative_reference_sequence_names_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

data SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier Source #

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Generic SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Show SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Eq SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier = D1 ('MetaData "SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier" "Data.SAM.Version1_6.Header.SQ" "hs-samtools-0.4.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

data SAM_V1_6_Reference_Sequence_Dictionary_Description Source #

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Generic SAM_V1_6_Reference_Sequence_Dictionary_Description Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Show SAM_V1_6_Reference_Sequence_Dictionary_Description Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Eq SAM_V1_6_Reference_Sequence_Dictionary_Description Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary_Description Source # 
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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 #

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Generic SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Show SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Eq SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum Source # 
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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 #

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Generic SAM_V1_6_Reference_Sequence_Dictionary_Species Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Show SAM_V1_6_Reference_Sequence_Dictionary_Species Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Eq SAM_V1_6_Reference_Sequence_Dictionary_Species Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary_Species Source # 
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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 #

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Generic SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Show SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Eq SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology Source # 
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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-0.4.0.0-inplace" 'False) (C1 ('MetaCons "SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology" 'PrefixI 'True) (S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_molecule_topology_tag") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 (Seq Word8)) :*: S1 ('MetaSel ('Just "sam_v1_6_reference_sequence_dictionary_molecule_topology_value") 'NoSourceUnpackedness 'NoSourceStrictness 'DecidedLazy) (Rec0 ByteString)))

data SAM_V1_6_Reference_Sequence_Dictionary_URI Source #

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Generic SAM_V1_6_Reference_Sequence_Dictionary_URI Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Show SAM_V1_6_Reference_Sequence_Dictionary_URI Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

Eq SAM_V1_6_Reference_Sequence_Dictionary_URI Source # 
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Defined in Data.SAM.Version1_6.Header.SQ

type Rep SAM_V1_6_Reference_Sequence_Dictionary_URI Source # 
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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)))