VcfJmx

##Motivation

Monitor/interrupt/break a VCF stream with java JMX http://www.oracle.com/technetwork/articles/java/javamanagement-140525.html . When multiple workflows are running, this tool gives the opportunity to visualize the current context in a jconsole ( https://docs.oracle.com/javase/7/docs/technotes/guides/management/jconsole.html ) and to interrupt the stream.

##Compilation

See also Compilation.

$  make vcfjmx

##Synopsis

$ java -jar dist/vcfjmx.jar (stdin|file) 

##Options

Option	Description
-p (stream-identifier)	will be displayed in the JMX console to identify the stream, Optional.
-h	get help (this screen) and exit.
-v	print version and exit.
-L (level)	log level. One of java.util.logging.Level . Optional.

##Source Code

Main code is: https://github.com/lindenb/jvarkit/blob/master/src/main/java/com/github/lindenb/jvarkit/tools/jmx/VcfJmx.java

##Example

$   java -jar dist/vcfjmx.jar -p MyWorkflow1 input.vcf > /dev/null

while the stream is running, open a new jconsole https://docs.oracle.com/javase/7/docs/technotes/guides/management/jconsole.html . here you can get the number of records, the elapsed time. Two operation are available:

• doBreak: interrupt current streaming , exit with success (0)
• doAbort: interrupt current streaming , exit with failure (-1)

Contribute

• Issue Tracker: http://github.com/lindenb/jvarkit/issues
• Source Code: http://github.com/lindenb/jvarkit

##See also

• http://plindenbaum.blogspot.fr/2015/05/monitoring-java-application-with-mbeans.html
• SamJmx

##History

• 2015 : Creation

License

The project is licensed under the MIT license.