jvarkit

SamJmx

Monitor/interrupt/break a BAM/SAM stream with java JMX http://www.oracle.com/technetwork/articles/java/javamanagement-140525.html

Usage

Usage: samjmx [options] Files
  Options:
    --bamcompression
      Compression Level.
      Default: 5
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    -o, --out
      Output file. Optional . Default: stdout
    --samoutputformat
      Sam output format.
      Default: SAM
      Possible Values: [BAM, SAM, CRAM]
    --version
      print version and exit
    -p
      Stream identifier

Keywords

• sam
• bam
• jmx
• monitoring

Compilation

Requirements / Dependencies

• java compiler SDK 11. Please check that this java is in the ${PATH}. Setting JAVA_HOME is not enough : (e.g: https://github.com/lindenb/jvarkit/issues/23 )

Download and Compile

$ git clone "https://github.com/lindenb/jvarkit.git"
$ cd jvarkit
$ ./gradlew samjmx

The java jar file will be installed in the dist directory.

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/jmx/SamJmx.java

Contribute

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

License

The project is licensed under the MIT license.

Citing

Should you cite samjmx ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

Example

$   java -jar dist/samjmx.jar  -T bam -p MyWorkflow1 input.bam > /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, t he elapsed time. Two operation are available:

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

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