public class SAMFileWriterFactory
extends java.lang.Object
implements java.lang.Cloneable
Constructor and Description |
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SAMFileWriterFactory()
simple constructor
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SAMFileWriterFactory(SAMFileWriterFactory other)
copy constructor
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Modifier and Type | Method and Description |
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SAMFileWriterFactory |
clone() |
int |
getCompressionLevel() |
static boolean |
getDefaultCreateIndexWhileWriting()
Gets the default for subsequent SAMFileWriterFactories that do not specify whether to create an index.
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static boolean |
getDefaultCreateMd5File()
Gets the default for whether to create md5Files for BAM files this factory.
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int |
getMaxRecordsInRam()
Gets the maximum number of records held in RAM before spilling to disk during sorting.
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java.io.File |
getTempDirectory()
Gets the temporary directory that will be used when sorting data.
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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.
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SAMFileWriter |
makeBAMWriter(SAMFileHeader header,
boolean presorted,
java.nio.file.Path outputPath)
Create a BAMFileWriter that is ready to receive SAMRecords.
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SAMFileWriter |
makeBAMWriter(SAMFileHeader header,
boolean presorted,
java.nio.file.Path outputPath,
int compressionLevel)
Create a BAMFileWriter that is ready to receive SAMRecords.
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CRAMFileWriter |
makeCRAMWriter(SAMFileHeader header,
boolean presorted,
java.io.File outputFile,
java.io.File referenceFasta)
Create a CRAMFileWriter on an output file.
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CRAMFileWriter |
makeCRAMWriter(SAMFileHeader header,
boolean presorted,
java.nio.file.Path output,
java.io.File referenceFasta)
Deprecated.
since 6/18, prefer
makeWriter(SAMFileHeader, boolean, Path, Path) for creating bam/cram writers
however makeCRAMWriter(SAMFileHeader, boolean, Path, Path) is the direct replacement for this method |
CRAMFileWriter |
makeCRAMWriter(SAMFileHeader header,
boolean presorted,
java.nio.file.Path output,
java.nio.file.Path referenceFasta)
Create a CRAMFileWriter on an output file.
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CRAMFileWriter |
makeCRAMWriter(SAMFileHeader header,
java.io.File outputFile,
java.io.File referenceFasta)
Create a CRAMFileWriter on an output file.
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CRAMFileWriter |
makeCRAMWriter(SAMFileHeader header,
java.io.OutputStream stream,
java.io.File referenceFasta)
Create a CRAMFileWriter on an output stream.
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CRAMFileWriter |
makeCRAMWriter(SAMFileHeader header,
java.io.OutputStream stream,
java.nio.file.Path referenceFasta)
Create a CRAMFileWriter on an output stream.
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CRAMFileWriter |
makeCRAMWriter(SAMFileHeader header,
java.nio.file.Path outputPath,
java.io.File referenceFasta)
Deprecated.
since 6/18, prefer
makeWriter(SAMFileHeader, boolean, Path, Path) for creating bam/cram writers
however makeCRAMWriter(SAMFileHeader, boolean, Path, Path) is the direct replacement for this method |
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 |
makeSAMOrBAMWriter(SAMFileHeader header,
boolean presorted,
java.nio.file.Path outputPath)
Create either a SAM or a BAM writer based on examination of the outputPath 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 |
makeSAMWriter(SAMFileHeader header,
boolean presorted,
java.nio.file.Path outputPath)
Create a SAMTextWriter that is ready to receive SAMRecords.
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SAMFileWriter |
makeWriter(SAMFileHeader header,
boolean presorted,
java.io.File outputFile,
java.io.File referenceFasta)
Create a SAM, BAM or CRAM writer based on examination of the outputFile extension.
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SAMFileWriter |
makeWriter(SAMFileHeader header,
boolean presorted,
java.nio.file.Path outputPath,
java.io.File referenceFasta)
Deprecated.
since 6/18, use
makeWriter(SAMFileHeader, boolean, Path, Path) instead |
SAMFileWriter |
makeWriter(SAMFileHeader header,
boolean presorted,
java.nio.file.Path outputPath,
java.nio.file.Path referenceFasta)
Create a SAM, BAM or CRAM writer based on examination of the outputPath extension.
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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 |
setCompressionLevel(int compressionLevel)
set compression level 0!none 9: max
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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 |
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 |
setDeflaterFactory(DeflaterFactory deflaterFactory)
Set the deflater factory used by BAM writers created by this writer 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 |
setSamFlagFieldOutput(SamFlagField samFlagFieldOutput)
Set the flag output format only when writing text.
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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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java.lang.String |
toString() |
public SAMFileWriterFactory()
public SAMFileWriterFactory(SAMFileWriterFactory other)
public SAMFileWriterFactory clone()
clone
in class java.lang.Object
public static void setDefaultCreateMd5File(boolean createMd5File)
public static boolean getDefaultCreateMd5File()
setDefaultCreateMd5File(boolean)
public SAMFileWriterFactory setCreateMd5File(boolean createMd5File)
public SAMFileWriterFactory setDeflaterFactory(DeflaterFactory deflaterFactory)
DeflaterFactory
is used which creates the default JDK Deflater
.
This method returns the SAMFileWriterFactory itself.public SAMFileWriterFactory setCompressionLevel(int compressionLevel)
public int getCompressionLevel()
public static void setDefaultCreateIndexWhileWriting(boolean setting)
setting
- whether to attempt to create a BAM index while creating the BAM filepublic static boolean getDefaultCreateIndexWhileWriting()
public 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 int getMaxRecordsInRam()
setMaxRecordsInRam(int)
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 java.io.File getTempDirectory()
setTempDirectory(File)
public SAMFileWriterFactory setSamFlagFieldOutput(SamFlagField samFlagFieldOutput)
public 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.nio.file.Path outputPath)
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.outputPath
- 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 makeBAMWriter(SAMFileHeader header, boolean presorted, java.nio.file.Path outputPath, 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.outputPath
- 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.nio.file.Path outputPath)
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.outputPath
- 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 makeSAMOrBAMWriter(SAMFileHeader header, boolean presorted, java.nio.file.Path outputPath)
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.outputPath
- 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)
header
- 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. Must end with .sam, .bam or .cram.referenceFasta
- reference sequence file@Deprecated public SAMFileWriter makeWriter(SAMFileHeader header, boolean presorted, java.nio.file.Path outputPath, java.io.File referenceFasta)
makeWriter(SAMFileHeader, boolean, Path, Path)
insteadheader
- 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.outputPath
- where to write the output. Must end with .sam, .bam or .cram.referenceFasta
- reference sequence filepublic SAMFileWriter makeWriter(SAMFileHeader header, boolean presorted, java.nio.file.Path outputPath, java.nio.file.Path referenceFasta)
header
- 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.outputPath
- where to write the output. Must end with .sam, .bam or .cram.referenceFasta
- reference sequence filepublic CRAMFileWriter makeCRAMWriter(SAMFileHeader header, java.io.OutputStream stream, java.io.File referenceFasta)
header
- entire header. Sort order is determined by the sortOrder property of this arg.stream
- where to write the output.referenceFasta
- reference sequence filepublic CRAMFileWriter makeCRAMWriter(SAMFileHeader header, java.io.OutputStream stream, java.nio.file.Path referenceFasta)
header
- entire header. Sort order is determined by the sortOrder property of this arg.stream
- where to write the output.referenceFasta
- reference sequence filepublic CRAMFileWriter makeCRAMWriter(SAMFileHeader header, java.io.File outputFile, java.io.File referenceFasta)
header
- entire header. Sort order is determined by the sortOrder property of this arg.outputFile
- where to write the output. Must end with .sam, .bam or .cram.referenceFasta
- reference sequence file@Deprecated public CRAMFileWriter makeCRAMWriter(SAMFileHeader header, java.nio.file.Path outputPath, java.io.File referenceFasta)
makeWriter(SAMFileHeader, boolean, Path, Path)
for creating bam/cram writers
however makeCRAMWriter(SAMFileHeader, boolean, Path, Path)
is the direct replacement for this methodheader
- entire header. Sort order is determined by the sortOrder property of this arg.outputPath
- where to write the output. Must end with .sam, .bam or .cram.referenceFasta
- reference sequence filepublic CRAMFileWriter makeCRAMWriter(SAMFileHeader header, boolean presorted, java.io.File outputFile, java.io.File referenceFasta)
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. Must end with .sam, .bam or .cram.referenceFasta
- reference sequence file@Deprecated public CRAMFileWriter makeCRAMWriter(SAMFileHeader header, boolean presorted, java.nio.file.Path output, java.io.File referenceFasta)
makeWriter(SAMFileHeader, boolean, Path, Path)
for creating bam/cram writers
however makeCRAMWriter(SAMFileHeader, boolean, Path, Path)
is the direct replacement for this methodheader
- 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.output
- where to write the output. Must end with .sam, .bam or .cram.referenceFasta
- reference sequence filepublic CRAMFileWriter makeCRAMWriter(SAMFileHeader header, boolean presorted, java.nio.file.Path output, java.nio.file.Path referenceFasta)
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.output
- where to write the output. Must end with .sam, .bam or .cram.referenceFasta
- reference sequence filepublic java.lang.String toString()
toString
in class java.lang.Object