a list of arguments to the JVM.
use advanced garbage collection parameters.
set the default validation stringency for Picard.
true if we are to use asynchronous IO, false otherwise.
the compress level to use.
true if we are to create an index, false otherwise.
true if we are to create an Md5 file, false otherwise.
the buffer size for the samjdk.
the buffer size for the samjdk.
Looks up the first super class that does not have "$anon$" in its name.
the compress level to use.
true if we are to create an index, false otherwise.
true if we are to create an Md5 file, false otherwise.
The path to the JAR to be executed.
a list of arguments to the JVM.
use advanced garbage collection parameters.
true if we are to use asynchronous IO, false otherwise.
set the default validation stringency for Picard.
Sets asynchronous IO on or off.
Sets the compression level to a specific value.
Sets asynchronous IO on or off.
Simple class to run any Picard command. Specific Picard command classes should extend this. Since the order of args is important to a task, an sub-class should call getPicardArgs before adding any tasks to args, and then call super.getTasks if getTasks is overriden.