Package | Description |
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htsjdk.samtools |
Modifier and Type | Interface and Description |
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interface |
BrowseableBAMIndex
An index interface with additional functionality for querying and inspecting the structure of a BAM index.
|
Modifier and Type | Class and Description |
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class |
AbstractBAMFileIndex
Provides basic, generic capabilities to be used reading BAM index files.
|
class |
SRAIndex
Emulates BAM index so that we can request chunks of records from SRAFileReader
Here is how it works:
SRA allows reading of alignments by Reference position fast, so we divide our "file" range for alignments as
a length of all references.
|
Modifier and Type | Method and Description |
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BAMIndex |
SRAFileReader.getIndex() |
BAMIndex |
CRAMFileReader.getIndex() |
BAMIndex |
SamReader.Indexing.getIndex()
Retrieves the index for the given file type.
|
BAMIndex |
SamReader.PrimitiveSamReader.getIndex() |
BAMIndex |
SamReader.PrimitiveSamReaderToSamReaderAdapter.getIndex() |
BAMIndex |
SAMFileReader.getIndex()
Deprecated.
Retrieves the index for the given file type.
|