Examples of org.broadinstitute.gatk.utils.progressmeter.ProgressMeter

• org.broadinstitute.gatk.utils.progressmeter.ProgressMeter
  A meter measuring progress on a calculation through a set of genomic regions that can print a few key metrics to a logger and optionally to a file The key information for assessing progress is a set of genome locs describing the total set of regions we will process. Whenever (at reasonable intervals) the processing unit can called notifyOfProgress and this logger may, depending on the metering delay, print a log message with the following metrics: -- Number of processed X (X = processing units) -- Runtime per.1M X -- Percent of regions to be processed completed -- The estimated total runtime based on previous performance -- The estimated time remaining for the entire process The optional file log an expanded set of metrics in tabular format suitable for subsequent analysis in R. This class is -- and MUST BE -- thread-safe for use in the GATK. Multiple independent threads executing processors will be calling notifyOfProgress() simultaneously and this class does (and MUST) properly sort out the timings of logs without interlacing outputs because of these threads. Consequently, the fundamental model for when to print the logs is time based. We basically print a meter message every X seconds, minutes, hours, whatever is appropriate based on the estimated remaining runtime. @author depristo @since 2010 maybe, but written in 09/12 for clarity

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