Package htsjdk.samtools
Interface SamReader.PrimitiveSamReader
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- All Known Implementing Classes:
BAMFileReader
,CRAMFileReader
,SamReader.ReaderImplementation
,SRAFileReader
- Enclosing interface:
- SamReader
public static interface SamReader.PrimitiveSamReader
The minimal subset of functionality needed for aSAMRecord
data source.SamReader
itself is somewhat large and bulky, but the core functionality can be captured in relatively few methods, which are included here. For documentation, see the corresponding methods inSamReader
. See also:SamReader.PrimitiveSamReaderToSamReaderAdapter
,SamReader.ReaderImplementation
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
close()
SAMFileHeader
getFileHeader()
SAMFileSpan
getFilePointerSpanningReads()
BAMIndex
getIndex()
CloseableIterator<SAMRecord>
getIterator()
CloseableIterator<SAMRecord>
getIterator(SAMFileSpan fileSpan)
ValidationStringency
getValidationStringency()
boolean
hasIndex()
CloseableIterator<SAMRecord>
query(QueryInterval[] intervals, boolean contained)
CloseableIterator<SAMRecord>
queryAlignmentStart(String sequence, int start)
CloseableIterator<SAMRecord>
queryUnmapped()
SamReader.Type
type()
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Method Detail
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type
SamReader.Type type()
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hasIndex
boolean hasIndex()
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getIndex
BAMIndex getIndex()
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getFileHeader
SAMFileHeader getFileHeader()
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getIterator
CloseableIterator<SAMRecord> getIterator()
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getIterator
CloseableIterator<SAMRecord> getIterator(SAMFileSpan fileSpan)
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getFilePointerSpanningReads
SAMFileSpan getFilePointerSpanningReads()
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query
CloseableIterator<SAMRecord> query(QueryInterval[] intervals, boolean contained)
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queryAlignmentStart
CloseableIterator<SAMRecord> queryAlignmentStart(String sequence, int start)
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queryUnmapped
CloseableIterator<SAMRecord> queryUnmapped()
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close
void close()
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getValidationStringency
ValidationStringency getValidationStringency()
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