Package org.snpeff.osCmd
Class OsCmdRunner
java.lang.Object
java.lang.Thread
org.snpeff.osCmd.OsCmdRunner
- All Implemented Interfaces:
Runnable
Run an OS command as a thread
- Author:
- pcingola
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Nested Class Summary
Nested classes/interfaces inherited from class java.lang.Thread
Thread.State, Thread.UncaughtExceptionHandler
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Field Summary
Fields inherited from class java.lang.Thread
MAX_PRIORITY, MIN_PRIORITY, NORM_PRIORITY
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionvoid
close()
Close (kill) commandvoid
finish()
Stop execution of this threadlong
getError()
int
getHead()
getJobId()
getOsCmd()
int
boolean
isDone()
Has this runner finished?boolean
void
run()
static boolean
runIfNotExists
(String[] opts, String outputFile, boolean redirectToOutput) Run an OS command only if the output files does not exists.boolean
runIfNotExists
(String outputFile, boolean redirectToOutput) Run a command only if 'outputFile' does not existvoid
setDefaultWaitTime
(long defaultWaitTime) void
setSaveStd
(boolean save) toString()
Methods inherited from class java.lang.Thread
activeCount, checkAccess, clone, countStackFrames, currentThread, dumpStack, enumerate, getAllStackTraces, getContextClassLoader, getDefaultUncaughtExceptionHandler, getId, getName, getPriority, getStackTrace, getState, getThreadGroup, getUncaughtExceptionHandler, holdsLock, interrupt, interrupted, isAlive, isDaemon, isInterrupted, join, join, join, onSpinWait, resume, setContextClassLoader, setDaemon, setDefaultUncaughtExceptionHandler, setName, setPriority, setUncaughtExceptionHandler, sleep, sleep, start, stop, suspend, yield
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Constructor Details
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OsCmdRunner
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Method Details
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runIfNotExists
Run an OS command only if the output files does not exists. opts[0] : OS Command opts[1] ... opts[N] : Command line options outputFile : Where the results are stored (if the file exists, the command is NOT run) redirect : If 'redirect=true' then run "command > outputFile" (i.e. redirect STDOUT to 'outputFile'). Output is assumed to be binary.- Parameters:
opts
-outputFile
-redirectToOutput
-- Returns:
- true if command executed OK or outputFile exists
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close
public void close()Close (kill) command -
finish
public void finish()Stop execution of this thread -
getDefaultWaitTime
public long getDefaultWaitTime() -
getError
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getExitValue
public int getExitValue() -
getHead
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getHeadStderr
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getJobId
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getOsCmd
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getProgress
public int getProgress() -
getStderr
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getStdout
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isDone
public boolean isDone()Has this runner finished?- Returns:
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isExecuting
public boolean isExecuting() -
run
public void run() -
runIfNotExists
Run a command only if 'outputFile' does not exist- Parameters:
outputFile
-redirectToOutput
-- Returns:
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setDefaultWaitTime
public void setDefaultWaitTime(long defaultWaitTime) -
setSaveStd
public void setSaveStd(boolean save) -
toString
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