public class SAMFileWriterFactory
extends java.lang.Object
Constructor and Description |
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SAMFileWriterFactory() |
Modifier and Type | Method and Description |
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SAMFileWriter |
makeBAMWriter(SAMFileHeader header,
boolean presorted,
java.io.File outputFile)
Create a BAMFileWriter that is ready to receive SAMRecords.
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SAMFileWriter |
makeBAMWriter(SAMFileHeader header,
boolean presorted,
java.io.File outputFile,
int compressionLevel)
Create a BAMFileWriter that is ready to receive SAMRecords.
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SAMFileWriter |
makeBAMWriter(SAMFileHeader header,
boolean presorted,
java.io.OutputStream stream)
Create a BAMFileWriter for writing to a stream that is ready to receive SAMRecords.
|
CRAMFileWriter |
makeCRAMWriter(SAMFileHeader header,
java.io.File outputFile,
java.io.File referenceFasta) |
CRAMFileWriter |
makeCRAMWriter(SAMFileHeader header,
java.io.OutputStream stream,
java.io.File referenceFasta) |
SAMFileWriter |
makeSAMOrBAMWriter(SAMFileHeader header,
boolean presorted,
java.io.File outputFile)
Create either a SAM or a BAM writer based on examination of the outputFile extension.
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SAMFileWriter |
makeSAMWriter(SAMFileHeader header,
boolean presorted,
java.io.File outputFile)
Create a SAMTextWriter that is ready to receive SAMRecords.
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SAMFileWriter |
makeSAMWriter(SAMFileHeader header,
boolean presorted,
java.io.OutputStream stream)
Create a SAMTextWriter for writing to a stream that is ready to receive SAMRecords.
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SAMFileWriter |
makeWriter(SAMFileHeader header,
boolean presorted,
java.io.File outputFile,
java.io.File referenceFasta) |
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 |
setBufferSize(int bufferSize)
Controls size of write buffer.
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SAMFileWriterFactory |
setCreateIndex(boolean setting)
Convenience method allowing newSAMFileWriterFactory().setCreateIndex(true);
Equivalent to SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(true); newSAMFileWriterFactory();
If a BAM (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 |
setCreateMd5File(boolean createMd5File)
Sets whether to create md5Files for BAMs from this factory.
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static void |
setDefaultCreateIndexWhileWriting(boolean setting)
Sets the default for subsequent SAMFileWriterFactories
that do not specify whether to create an index.
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static void |
setDefaultCreateMd5File(boolean createMd5File)
Sets the default for whether to create md5Files for BAM files this factory.
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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.
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SAMFileWriterFactory |
setTempDirectory(java.io.File tmpDir)
Set the temporary directory to use when sort data.
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SAMFileWriterFactory |
setUseAsyncIo(boolean useAsyncIo)
Turn on or off the use of asynchronous IO for writing output SAM and BAM files.
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public static void setDefaultCreateMd5File(boolean createMd5File)
public SAMFileWriterFactory setCreateMd5File(boolean createMd5File)
public static void setDefaultCreateIndexWhileWriting(boolean setting)
setting
- whether to attempt to create a BAM index while creating the BAM filepublic SAMFileWriterFactory setCreateIndex(boolean setting)
setting
- whether to attempt to create a BAM index while creating the BAM file.public SAMFileWriterFactory setMaxRecordsInRam(int maxRecordsInRam)
maxRecordsInRam
- Number of records to store in RAM before spilling to temporary file when
creating a sorted SAM or BAM file.public SAMFileWriterFactory setUseAsyncIo(boolean useAsyncIo)
public SAMFileWriterFactory setAsyncOutputBufferSize(int asyncOutputBufferSize)
public SAMFileWriterFactory setBufferSize(int bufferSize)
public SAMFileWriterFactory setTempDirectory(java.io.File tmpDir)
tmpDir
- Path to the temporary directorypublic SAMFileWriter makeBAMWriter(SAMFileHeader header, boolean presorted, java.io.File outputFile)
header
- entire header. Sort order is determined by the sortOrder property of this arg.presorted
- if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder.outputFile
- where to write the output.public SAMFileWriter makeBAMWriter(SAMFileHeader header, boolean presorted, java.io.File outputFile, int compressionLevel)
header
- entire header. Sort order is determined by the sortOrder property of this arg.presorted
- if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder.outputFile
- where to write the output.compressionLevel
- Override default compression level with the given value, between 0 (fastest) and 9 (smallest).public SAMFileWriter makeSAMWriter(SAMFileHeader header, boolean presorted, java.io.File outputFile)
header
- entire header. Sort order is determined by the sortOrder property of this arg.presorted
- if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder.outputFile
- where to write the output.public SAMFileWriter makeSAMWriter(SAMFileHeader header, boolean presorted, java.io.OutputStream stream)
header
- entire header. Sort order is determined by the sortOrder property of this arg.presorted
- if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder.stream
- the stream to write records to. Note that this method does not buffer the stream, so the
caller must buffer if desired. Note that PrintStream is buffered.public SAMFileWriter makeBAMWriter(SAMFileHeader header, boolean presorted, java.io.OutputStream stream)
header
- entire header. Sort order is determined by the sortOrder property of this arg.presorted
- if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder.stream
- the stream to write records to. Note that this method does not buffer the stream, so the
caller must buffer if desired. Note that PrintStream is buffered.public SAMFileWriter makeSAMOrBAMWriter(SAMFileHeader header, boolean presorted, java.io.File outputFile)
header
- entire header. Sort order is determined by the sortOrder property of this arg.presorted
- presorted if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder.outputFile
- where to write the output. Must end with .sam or .bam.public SAMFileWriter makeWriter(SAMFileHeader header, boolean presorted, java.io.File outputFile, java.io.File referenceFasta)
public CRAMFileWriter makeCRAMWriter(SAMFileHeader header, java.io.OutputStream stream, java.io.File referenceFasta)
public CRAMFileWriter makeCRAMWriter(SAMFileHeader header, java.io.File outputFile, java.io.File referenceFasta)