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.
Looks up the first super class that does not have "$anon$" in its name.
the compress level to use.
the compress level to use.
true if we are to create an index, false otherwise.
true if we are to create an index, false otherwise.
true if we are to create an Md5 file, false otherwise.
true if we are to create an Md5 file, false otherwise.
The path to the input BAM
The path to the input BAM
The path to the JAR to be executed.
The path to the JAR to be executed.
a list of arguments to the JVM.
a list of arguments to the JVM.
All Picard metric generating tools should define their own metrics extension.
All Picard metric generating tools should define their own metrics extension.
Build a path to a metrics file (text of PDF) using the appropriate prefix derived from either the supplied prefix, or the input file name.
Build a path to a metrics file (text of PDF) using the appropriate prefix derived from either the supplied prefix, or the input file name. Useful when a program produces multiple outputs, as in the case of CollectGcBiasMetrics.
Gets the metrics file path, assuming that the program generates a single metrics file with a known extension.
Gets the metrics file path, assuming that the program generates a single metrics file with a known extension.
Method that should be used to fetch the file prefix, instead of accessing prefix
directly.
Method that should be used to fetch the file prefix, instead of accessing prefix
directly.
The optional path to the prefix of the metrics file
The optional path to the prefix of the metrics file
use advanced garbage collection parameters.
use advanced garbage collection parameters.
true if we are to use asynchronous IO, false otherwise.
true if we are to use asynchronous IO, false otherwise.
set the default validation stringency for Picard.
set the default validation stringency for Picard.
Sets asynchronous IO on or off.
Sets asynchronous IO on or off.
Sets the compression level to a specific value.
Sets the compression level to a specific value.
Sets asynchronous IO on or off.
Sets asynchronous IO on or off.
Note: if no prefix is given, the metrics file will be named based on the first BAM in
inputs
.