zzh
/
gatk-3.8
1
0
Fork 0
Code Issues Pull Requests Packages Projects Releases Wiki Activity

Merge pull request #645 from broadinstitute/pd_progress_format 

Legibility improvements to ProgressMeter
This commit is contained in:
Eric Banks 2014-05-28 08:45:26 -04:00
parent b77589696e 6122b2805d
commit ed66f690dd
1 changed files with 19 additions and 5 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

24
public/gatk-tools-public/src/main/java/org/broadinstitute/gatk/utils/progressmeter/ProgressMeter.java
View File

@ -136,6 +136,16 @@ public class ProgressMeter {
*/
private final String processingUnitName;
/**
* The space allocated to #processingUnitName in the output
*/
private final int processingUnitWidth;
/**
* The format string used for progress lines
*/
private final String progressFormatString;
/**
* A potentially null file where we print a supplementary, R readable performance log
* file.
@ -181,6 +191,8 @@ public class ProgressMeter {
this.processingUnitName = processingUnitName;
this.regionsBeingProcessed = processingIntervals;
this.processingUnitWidth = Math.max(processingUnitName.length(), "processed".length());
this.progressFormatString = String.format("%%15s %%%1$ds %%7s %%%1$ds %%5.1f%%%% %%7s %%9s", processingUnitWidth);
// setup the performance logger output, if requested
if ( performanceLogFile != null ) {
@ -215,10 +227,12 @@ public class ProgressMeter {
public synchronized void start() {
timer.start();
lastProgressPrintTime = timer.currentTime();
final String formatString = String.format("%%15s | %%%1$ds | %%7s | %%%1$ds | %%9s | %%7s | %%9s", processingUnitWidth);
logger.info("[INITIALIZATION COMPLETE; STARTING PROCESSING]");
logger.info(String.format("%15s processed.%s runtime per.1M.%s completed total.runtime remaining",
"Location", processingUnitName, processingUnitName));
logger.info(String.format(formatString, "", "processed", "time", "per 1M", "", "total", "remaining"));
logger.info(String.format(formatString, "Location", processingUnitName, "elapsed", processingUnitName,
"completed", "runtime", "runtime"));
progressMeterDaemon.start();
}
@ -362,18 +376,18 @@ public class ProgressMeter {
if ( printProgress || printLog ) {
final ProgressMeterData progressData = takeProgressSnapshot(maxGenomeLoc, nTotalRecordsProcessed);
final AutoFormattingTime elapsed = new AutoFormattingTime(progressData.getElapsedSeconds());
final AutoFormattingTime elapsed = new AutoFormattingTime(progressData.getElapsedSeconds(), 5, 1);
final AutoFormattingTime bpRate = new AutoFormattingTime(progressData.secondsPerMillionBP());
final AutoFormattingTime unitRate = new AutoFormattingTime(progressData.secondsPerMillionElements());
final double fractionGenomeTargetCompleted = progressData.calculateFractionGenomeTargetCompleted(targetSizeInBP);
final AutoFormattingTime estTotalRuntime = new AutoFormattingTime(elapsed.getTimeInSeconds() / fractionGenomeTargetCompleted);
final AutoFormattingTime estTotalRuntime = new AutoFormattingTime(elapsed.getTimeInSeconds() / fractionGenomeTargetCompleted, 5, 1);
final AutoFormattingTime timeToCompletion = new AutoFormattingTime(estTotalRuntime.getTimeInSeconds() - elapsed.getTimeInSeconds());
if ( printProgress ) {
lastProgressPrintTime = curTime;
updateLoggerPrintFrequency(estTotalRuntime.getTimeInSeconds());
logger.info(String.format("%15s %5.2e %s %s %5.1f%% %s %s",
logger.info(String.format(progressFormatString,
position.getMessage(), progressData.getUnitsProcessed()*1.0, elapsed, unitRate,
100*fractionGenomeTargetCompleted, estTotalRuntime, timeToCompletion));