Package | Description |
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htsjdk.samtools |
Modifier and Type | Method and Description |
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SAMFileWriterFactory |
SAMFileWriterFactory.clone() |
SAMFileWriterFactory |
SAMFileWriterFactory.setAsyncOutputBufferSize(int asyncOutputBufferSize)
If and only if using asynchronous IO then sets the maximum number of records that can be buffered per
SAMFileWriter before producers will block when trying to write another SAMRecord.
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SAMFileWriterFactory |
SAMFileWriterFactory.setBufferSize(int bufferSize)
Controls size of write buffer.
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SAMFileWriterFactory |
SAMFileWriterFactory.setCreateIndex(boolean setting)
Convenience method allowing newSAMFileWriterFactory().setCreateIndex(true);
Equivalent to SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(true); newSAMFileWriterFactory();
If a BAM or CRAM (not SAM) file is created, the setting is true, and the file header specifies coordinate order,
then a BAM index file will be written along with the BAM file.
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SAMFileWriterFactory |
SAMFileWriterFactory.setCreateMd5File(boolean createMd5File)
Sets whether to create md5Files for BAMs from this factory.
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SAMFileWriterFactory |
SAMFileWriterFactory.setMaxRecordsInRam(int maxRecordsInRam)
Before creating a writer that is not presorted, this method may be called in order to override
the default number of SAMRecords stored in RAM before spilling to disk
(c.f.
|
SAMFileWriterFactory |
SAMFileWriterFactory.setTempDirectory(File tmpDir)
Set the temporary directory to use when sort data.
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SAMFileWriterFactory |
SAMFileWriterFactory.setUseAsyncIo(boolean useAsyncIo)
Turn on or off the use of asynchronous IO for writing output SAM and BAM files.
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Constructor and Description |
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SAMFileWriterFactory(SAMFileWriterFactory other)
copy constructor
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