Package htsjdk.beta.io.bundle
Class BundleResourceType
java.lang.Object
htsjdk.beta.io.bundle.BundleResourceType
Constants for specifying standard content types and formats for resources contained in a
Bundle
.
Bundles generally contain one primary resource, plus one or more secondary resources such as an index or md5 file.
Each resource has an associated content type, and optionally a format. The bundle itself has a primary content
type, which is the content type of the primary resource (and the bundle must always contain a resource with the
content type that corresponds to the primary content type of the bundle).
Although any string can be used as a primary content type in a bundle, the standard primary content types generally
correspond to one of the enum values in HtsContentType
, since each of these has a
corresponding HtsCodec
that handles that type of resource, such as reads or variants.
Secondary resource content types can also be any string, but the standard secondary content types are defined
here, i.e., for primary content type "READS", a secondary content type might be "READS_INDEX".
Finally, each resource in a bundle can have an optional format, which is a string that corresponds to the format
for that resource. For example, a primary content type of "READS" might have a format of "BAM".-
Field Summary
FieldsModifier and TypeFieldDescriptionstatic final String
Common primary content typesstatic final String
static final String
static final String
MISCELLANEOUS Resource typesstatic final String
Secondary content types names for content typeCT_ALIGNED_READS
resourcesstatic final String
Secondary content types forCT_HAPLOID_REFERENCE
resourcesstatic final String
static final String
static final String
Secondary content types for primary content typeCT_VARIANT_CONTEXTS
resourcesstatic final String
static final String
static final String
static final String
Formats for secondary content typeCT_READS_INDEX
resourcesstatic final String
static final String
static final String
Formats for primary content typeCT_ALIGNED_READS
static final String
static final String
Format names for content typeCT_VARIANT_CONTEXTS
-
Constructor Summary
Constructors -
Method Summary
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Field Details
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CT_ALIGNED_READS
Common primary content types- See Also:
-
CT_VARIANT_CONTEXTS
- See Also:
-
CT_HAPLOID_REFERENCE
- See Also:
-
CT_FEATURES
- See Also:
-
FMT_READS_SAM
Formats for primary content typeCT_ALIGNED_READS
- See Also:
-
FMT_READS_BAM
- See Also:
-
FMT_READS_CRAM
- See Also:
-
FMT_READS_HTSGET_BAM
- See Also:
-
CT_READS_INDEX
Secondary content types names for content typeCT_ALIGNED_READS
resources- See Also:
-
FMT_READS_INDEX_BAI
Formats for secondary content typeCT_READS_INDEX
resources- See Also:
-
FMT_READS_INDEX_CRAI
- See Also:
-
FMT_READS_INDEX_CSI
- See Also:
-
FMT_VARIANTS_VCF
Format names for content typeCT_VARIANT_CONTEXTS
- See Also:
-
FMT_VARIANTS_BCF
- See Also:
-
CT_VARIANTS_INDEX
Secondary content types for primary content typeCT_VARIANT_CONTEXTS
resources- See Also:
-
CT_REFERENCE_DICTIONARY
Secondary content types forCT_HAPLOID_REFERENCE
resources- See Also:
-
CT_REFERENCE_INDEX
- See Also:
-
CT_MD5
MISCELLANEOUS Resource types- See Also:
-
-
Constructor Details
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BundleResourceType
public BundleResourceType()
-