Package | Description |
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htsjdk.samtools | |
htsjdk.samtools.cram.build | |
htsjdk.samtools.cram.ref |
Modifier and Type | Method and Description |
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abstract ReferenceSource |
SamReaderFactory.referenceSource() |
Modifier and Type | Method and Description |
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abstract SamReaderFactory |
SamReaderFactory.referenceSource(ReferenceSource referenceSequence)
Sets the specified reference sequence *
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Constructor and Description |
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CRAMContainerStreamWriter(OutputStream outputStream,
OutputStream indexStream,
ReferenceSource source,
SAMFileHeader samFileHeader,
String cramId)
Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM
containers on output stream, with an optional index.
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CRAMFileReader(File cramFile,
File indexFile,
ReferenceSource referenceSource)
Create a CRAMFileReader from a file and optional index file using the supplied reference source.
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CRAMFileReader(File cramFile,
File indexFile,
ReferenceSource referenceSource,
ValidationStringency validationStringency)
Create a CRAMFileReader from a CRAM file and optional index file using the supplied reference
source and validation stringency.
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CRAMFileReader(File cramFile,
InputStream inputStream,
ReferenceSource referenceSource)
Create a CRAMFileReader from either a file or input stream using the supplied reference source.
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CRAMFileReader(File cramFile,
ReferenceSource referenceSource)
Create a CRAMFileReader from a file using the supplied reference source.
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CRAMFileReader(InputStream stream,
File indexFile,
ReferenceSource referenceSource,
ValidationStringency validationStringency)
Create a CRAMFileReader from an input stream and optional index file using the supplied reference
source and validation stringency.
|
CRAMFileReader(InputStream inputStream,
SeekableStream indexInputStream,
ReferenceSource referenceSource,
ValidationStringency validationStringency)
Create a CRAMFileReader from an input stream and optional index stream using the supplied reference
source and validation stringency.
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CRAMFileWriter(OutputStream outputStream,
OutputStream indexOS,
boolean presorted,
ReferenceSource referenceSource,
SAMFileHeader samFileHeader,
String fileName)
Create a CRAMFileWriter and optional index on output streams.
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CRAMFileWriter(OutputStream outputStream,
OutputStream indexOS,
ReferenceSource referenceSource,
SAMFileHeader samFileHeader,
String fileName)
Create a CRAMFileWriter and optional index on output streams.
|
CRAMFileWriter(OutputStream outputStream,
ReferenceSource referenceSource,
SAMFileHeader samFileHeader,
String fileName)
Create a CRAMFileWriter on an output stream.
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CRAMIterator(InputStream inputStream,
ReferenceSource referenceSource,
ValidationStringency validationStringency) |
CRAMIterator(SeekableStream seekableStream,
ReferenceSource referenceSource,
long[] coordinates)
Deprecated.
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CRAMIterator(SeekableStream seekableStream,
ReferenceSource referenceSource,
long[] coordinates,
ValidationStringency validationStringency) |
Constructor and Description |
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CramNormalizer(SAMFileHeader header,
ReferenceSource referenceSource) |
Modifier and Type | Method and Description |
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static ReferenceSource |
ReferenceSource.getDefaultCRAMReferenceSource()
Attempts to construct a default ReferenceSource for use with CRAM files when
one has not been explicitly provided.
|