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Fix for inaccurate and misleading timing information, now only prints estimated time to completion when the location flag isn't set 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@25 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2009-03-10 14:59:42 +00:00
parent 17c94a8c5c
commit e4bde58353
3 changed files with 28 additions and 9 deletions
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29
java/src/edu/mit/broad/sting/atk/TraversalEngine.java
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@ -31,6 +31,8 @@ public class TraversalEngine {
private ValidationStringency strictness = ValidationStringency.STRICT;
private long startTime = -1;
private long lastProgressPrintTime = -1;
private long MAX_PROGRESS_PRINT_TIME = 5 * 1000; // 10 seconds in millisecs
private long maxReads = -1;
private long nRecords = 0;
private SAMFileReader samReader = null;
@ -63,7 +65,7 @@ public class TraversalEngine {
}
protected int initialize() {
startTime = System.currentTimeMillis();
lastProgressPrintTime = startTime = System.currentTimeMillis();
loadReference();
//testReference();
//loadReference();
@ -146,19 +148,34 @@ public class TraversalEngine {
// functions for dealing with the reference sequence
//
// --------------------------------------------------------------------------------------------------------------
/**
*
* @param curTime (current runtime, in millisecs)
* @return true if the maximum interval (in millisecs) has passed since the last printing
*/
private boolean maxElapsedIntervalForPrinting(final long curTime) {
return (curTime - this.lastProgressPrintTime) > MAX_PROGRESS_PRINT_TIME;
}
public void printProgress(final String type, GenomeLoc loc) { printProgress( false, type, loc ); }
public void printProgress( boolean mustPrint, final String type, GenomeLoc loc ) {
final long nRecords = this.nRecords;
final long curTime = System.currentTimeMillis();
final double elapsed = (curTime - startTime) / 1000.0;
//System.out.printf("Cur = %d, last print = %d%n", curTime, lastProgressPrintTime);
if ( mustPrint || nRecords % 100000 == 0 ) {
final double elapsed = (System.currentTimeMillis() - startTime) / 1000.0;
if ( mustPrint || nRecords % 100000 == 0 || maxElapsedIntervalForPrinting(curTime)) {
this.lastProgressPrintTime = curTime;
final double secsPer1MReads = (elapsed * 1000000.0) / nRecords;
if ( loc != null )
System.out.printf("Traversed to %s, processing %d %s %.2f secs (%.2f secs per 1M %s)%n", loc, nRecords, type, elapsed, secsPer1MReads, type);
System.out.printf("[PROGRESS] Traversed to %s, processing %d %s %.2f secs (%.2f secs per 1M %s)%n", loc, nRecords, type, elapsed, secsPer1MReads, type);
else
System.out.printf("Traversed %d %s %.2f secs (%.2f secs per 1M %s)%n", nRecords, type, elapsed, secsPer1MReads, type);
System.out.printf(" -> %s%n", samReadingTracker.progressMeter());
System.out.printf("[PROGRESS] Traversed %d %s %.2f secs (%.2f secs per 1M %s)%n", nRecords, type, elapsed, secsPer1MReads, type);
if ( this.locs == null )
System.out.printf("[PROGRESS] -> %s%n", samReadingTracker.progressMeter());
}
}

4
java/src/edu/mit/broad/sting/utils/FileProgressTracker.java
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@ -144,8 +144,8 @@ public class FileProgressTracker<T> implements Iterator<T> {
//printStatus();
return String.format("Est. %.2f%% completed, time remaining (%.2f hrs / %.2f min) of (%.2f hrs / %.2f min) total",
estFractionProgressThroughFile() * 100.0,
estTimeTotal() / (60*60), estTimeTotal() / (60),
estTimeRemaining() / (60*60), estTimeRemaining() / 60);
estTimeRemaining() / (60*60), estTimeRemaining() / 60,
estTimeTotal() / (60*60), estTimeTotal() / (60));
}
public ArrayList<Long> recordSizes() {

2
scripts/buildRODs.sh 100755
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@ -0,0 +1,2 @@
java -Xmx40000m -cp out/production/AnalysisTK:trunk/java/jars/functionalj.jar edu.mit.broad.sting.atk.PrepareROD REF_FILE_ARG=/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta ROD_FILE=/seq/references/dbsnp/downloads/snp129_hg18.txt OUT=`echo $1/snp129_hg18.txt.rod` ROD_TYPE=dbSNP ROD_NAME=dbSNP