@DocumentedFeature public class FifoBuffer extends CommandLineProgram
java -jar SamToFastq.jar \ F=my.fastq \ INTERLEAVE=true | java -jar FifoBuffer | bwa mem -t 8 -Y reference.fasta \dev\stdin output.bam
Modifier and Type | Field and Description |
---|---|
int |
BUFFER_SIZE |
int |
DEBUG_FREQUENCY |
int |
IO_SIZE |
java.lang.String |
NAME |
COMPRESSION_LEVEL, CREATE_INDEX, CREATE_MD5_FILE, GA4GH_CLIENT_SECRETS, MAX_RECORDS_IN_RAM, QUIET, REFERENCE_SEQUENCE, referenceSequence, specialArgumentsCollection, TMP_DIR, USE_JDK_DEFLATER, USE_JDK_INFLATER, VALIDATION_STRINGENCY, VERBOSITY
Constructor and 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(java.io.InputStream in,
java.io.PrintStream out)
Constructor that defaults to QUIET since Fifos don't do anything beyond buffering having their
start/end information logged is often undesirable.
|
Modifier and Type | Method and Description |
---|---|
protected int |
doWork()
Do the work after command line has been parsed.
|
static void |
main(java.lang.String[] args) |
customCommandLineValidation, getCommandLine, getCommandLineParser, getDefaultHeaders, getFaqLink, getMetricsFile, getStandardUsagePreamble, getStandardUsagePreamble, getVersion, hasWebDocumentation, instanceMain, instanceMainWithExit, makeReferenceArgumentCollection, parseArgs, requiresReference, setDefaultHeaders, useLegacyParser
@Argument(doc="The size of the memory buffer in bytes.") public int BUFFER_SIZE
@Argument(doc="The size, in bytes, to read/write atomically to the input and output streams.") public int IO_SIZE
@Argument(doc="How frequently, in seconds, to report debugging statistics. Set to zero for never.") public int DEBUG_FREQUENCY
@Argument(doc="Name to use for Fifo in debugging statements.", optional=true) public java.lang.String NAME
public FifoBuffer(java.io.InputStream in, java.io.PrintStream out)
public FifoBuffer()
public static void main(java.lang.String[] args)
protected int doWork()
CommandLineProgram
doWork
in class CommandLineProgram