Data.SAM.Version1_6.Header.SQ

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.

SAM version 1.6 Reference sequence dictionary data type

data SAM_V1_6_Reference_Sequence_Dictionary

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

SAM_V1_6_Reference_Sequence_Dictionary

Fields

• 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

SAM version 1.6 Reference sequence dictionary data types

data SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name

SN tag for SAM_V1_6_Reference_Sequence_Dictionary.

Constructors

SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Name

Fields

• sam_v1_6_reference_sequence_dictionary_reference_sequence_name_tag :: Seq Word8
• sam_v1_6_reference_sequence_dictionary_reference_sequence_name_value :: ByteString

data SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length

LN tag for SAM_V1_6_Reference_Sequence_Dictionary.

Constructors

SAM_V1_6_Reference_Sequence_Dictionary_Reference_Sequence_Length

Fields

• sam_v1_6_reference_sequence_dictionary_reference_sequence_length_tag :: Seq Word8
• sam_v1_6_reference_sequence_dictionary_reference_sequence_length_value :: ByteString

data SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus

AH tag for SAM_V1_6_Reference_Sequence_Dictionary.

Constructors

SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Locus

Fields

• sam_v1_6_reference_sequence_dictionary_reference_alternative_locus_tag :: Seq Word8
• sam_v1_6_reference_sequence_dictionary_reference_alternative_locus_value :: ByteString

data SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names

AN tag for SAM_V1_6_Reference_Sequence_Dictionary.

Constructors

SAM_V1_6_Reference_Sequence_Dictionary_Alternative_Reference_Sequence_Names

Fields

• sam_v1_6_reference_sequence_dictionary_reference_alternative_reference_sequence_names_tag :: Seq Word8
• sam_v1_6_reference_sequence_dictionary_reference_alternative_reference_sequence_names_value :: ByteString

data SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier

AS tag for SAM_V1_6_Reference_Sequence_Dictionary.

Constructors

SAM_V1_6_Reference_Sequence_Dictionary_Genome_Assembly_Identifier

Fields

• sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_tag :: Seq Word8
• sam_v1_6_reference_sequence_dictionary_genome_assembly_identifier_value :: ByteString

data SAM_V1_6_Reference_Sequence_Dictionary_Description

DS tag for SAM_V1_6_Reference_Sequence_Dictionary.

Constructors

SAM_V1_6_Reference_Sequence_Dictionary_Description

Fields

• sam_v1_6_reference_sequence_dictionary_description_tag :: Seq Word8
• sam_v1_6_reference_sequence_dictionary_description_value :: ByteString

data SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum

M5 tag for SAM_V1_6_Reference_Sequence_Dictionary.

Constructors

SAM_V1_6_Reference_Sequence_Dictionary_MD5_Checksum

Fields

• sam_v1_6_reference_sequence_dictionary_md5_checksum_tag :: Seq Word8
• sam_v1_6_reference_sequence_dictionary_md5_checksum_value :: ByteString

data SAM_V1_6_Reference_Sequence_Dictionary_Species

SP tag for SAM_V1_6_Reference_Sequence_Dictionary.

Constructors

SAM_V1_6_Reference_Sequence_Dictionary_Species

Fields

• sam_v1_6_reference_sequence_dictionary_species_tag :: Seq Word8
• sam_v1_6_reference_sequence_dictionary_species_value :: ByteString

data SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology

TP tag for SAM_V1_6_Reference_Sequence_Dictionary.

Constructors

SAM_V1_6_Reference_Sequence_Dictionary_Molecule_Topology

Fields

• sam_v1_6_reference_sequence_dictionary_molecule_topology_tag :: Seq Word8
• sam_v1_6_reference_sequence_dictionary_molecule_topology_value :: ByteString

data SAM_V1_6_Reference_Sequence_Dictionary_URI

UR tag for SAM_V1_6_Reference_Sequence_Dictionary.

Constructors

SAM_V1_6_Reference_Sequence_Dictionary_URI

Fields

• sam_v1_6_reference_sequence_dictionary_uri_tag :: Seq Word8
• sam_v1_6_reference_sequence_dictionary_uri_value :: ByteString