Package picard.util
Class FifoBuffer
java.lang.Object
picard.cmdline.CommandLineProgram
picard.util.FifoBuffer
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
FieldsFields 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, SYNTAX_TRANSITION_URL, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
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Constructor Summary
ConstructorsConstructorDescriptionConstructor 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. -
Method Summary
Modifier and TypeMethodDescriptionprotected int
doWork()
Do the work after command line has been parsed.Methods inherited from class picard.cmdline.CommandLineProgram
checkRInstallation, customCommandLineValidation, getCommandLine, getCommandLineParser, getCommandLineParserForArgs, getDefaultHeaders, getFaqLink, getMetricsFile, getPGRecord, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
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Field Details
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BUFFER_SIZE
@Argument(doc="The size of the memory buffer in bytes.") public int BUFFER_SIZE -
IO_SIZE
@Argument(doc="The size, in bytes, to read/write atomically to the input and output streams.") public int IO_SIZE -
DEBUG_FREQUENCY
@Argument(doc="How frequently, in seconds, to report debugging statistics. Set to zero for never.") public int DEBUG_FREQUENCY -
NAME
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Constructor Details
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FifoBuffer
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their start/end information logged is often undesirable. -
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 Details
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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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