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Code Block
languagebash
export JAVA_OPTS="-DdisableSvtAlignmentConstants=trueDorg.hps.conditions.enableSvtAlignmentConstants"

The full list of Java system properties to be used should be included in this variable.  You should not set the options -Xmx or -Djava.util.logging.config.class, as these are set by each script.

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