Package htsjdk.samtools
Interface SAMFileWriter
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- All Superinterfaces:
AutoCloseable
,Closeable
- All Known Implementing Classes:
BAMFileWriter
,CRAMFileWriter
,SAMFileWriterImpl
,SAMTextWriter
public interface SAMFileWriter extends Closeable
Interface for SAMText and BAM file writers. Clients need not care which they write to, once the object is constructed.
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
addAlignment(SAMRecord alignment)
void
close()
Must be called to flush or file will likely be defective.SAMFileHeader
getFileHeader()
void
setProgressLogger(ProgressLoggerInterface progress)
Sets a ProgressLogger on this writer.
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Method Detail
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addAlignment
void addAlignment(SAMRecord alignment)
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getFileHeader
SAMFileHeader getFileHeader()
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setProgressLogger
void setProgressLogger(ProgressLoggerInterface progress)
Sets a ProgressLogger on this writer. This is useful when pulling, for instance, from a SortingCollection.
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close
void close()
Must be called to flush or file will likely be defective.- Specified by:
close
in interfaceAutoCloseable
- Specified by:
close
in interfaceCloseable
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