Package picard.util
Class FifoBuffer
- java.lang.Object
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- picard.cmdline.CommandLineProgram
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- picard.util.FifoBuffer
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@DocumentedFeature public class FifoBuffer extends CommandLineProgram
Summary
Acts as a large memory buffer between processes that are connected with unix pipes for the case that one or more processes produces or consumes their input or output in bursts. By inserting a large memory buffer between such processes each process can run at full speed and the bursts can be smoothed out by the memory buffer.Example
java -jar SamToFastq.jar \ F=my.fastq \ INTERLEAVE=true | java -jar FifoBuffer | bwa mem -t 8 -Y reference.fasta \dev\stdin output.bam
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Field Summary
Fields Modifier and Type Field Description int
BUFFER_SIZE
int
DEBUG_FREQUENCY
int
IO_SIZE
String
NAME
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Fields inherited from class picard.cmdline.CommandLineProgram
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_ALLOWABLE_ONE_LINE_SUMMARY_LENGTH, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
Constructors Constructor Description FifoBuffer()
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable.FifoBuffer(InputStream in, PrintStream out)
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected int
doWork()
Do the work after command line has been parsed.-
Methods inherited from class picard.cmdline.CommandLineProgram
customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Detail
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BUFFER_SIZE
@Argument(doc="The size of the memory buffer in bytes.") public int BUFFER_SIZE
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IO_SIZE
@Argument(doc="The size, in bytes, to read/write atomically to the input and output streams.") public int IO_SIZE
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DEBUG_FREQUENCY
@Argument(doc="How frequently, in seconds, to report debugging statistics. Set to zero for never.") public int DEBUG_FREQUENCY
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NAME
@Argument(doc="Name to use for Fifo in debugging statements.", optional=true) public String NAME
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Constructor Detail
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FifoBuffer
public FifoBuffer(InputStream in, PrintStream out)
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable.
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FifoBuffer
public FifoBuffer()
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable.
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Method Detail
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doWork
protected int doWork()
Description copied from class:CommandLineProgram
Do the work after command line has been parsed. RuntimeException may be thrown by this method, and are reported appropriately.- Specified by:
doWork
in classCommandLineProgram
- Returns:
- program exit status.
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