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Bugfix for printProgress in TraverseReadsNano 

-- Must provide a single bp position (1:10) not the range of the read (1:1-50).  ProgressMeter now checks at runtime for this problem as well.
This commit is contained in:
Mark DePristo 2013-01-04 10:54:02 -05:00
parent 6af1e21758
commit a5901cdd20
2 changed files with 5 additions and 2 deletions
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3
public/java/src/org/broadinstitute/sting/gatk/traversals/TraverseReadsNano.java
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@ -65,7 +65,8 @@ public class TraverseReadsNano<M,T> extends TraversalEngine<M,T,ReadWalker<M,T>,
@Override @Override
public void progress(MapData lastProcessedMap) { public void progress(MapData lastProcessedMap) {
if ( lastProcessedMap.refContext != null ) if ( lastProcessedMap.refContext != null )
printProgress(lastProcessedMap.refContext.getLocus()); // note, need to use getStopLocation so we don't give an interval to ProgressMeterDaemon
printProgress(lastProcessedMap.refContext.getLocus().getStopLocation());
} }
}); });
} }

4
public/java/src/org/broadinstitute/sting/utils/progressmeter/ProgressMeter.java
View File

@ -234,11 +234,13 @@ public class ProgressMeter {
* the progress itself. A separate printing daemon periodically polls the meter to print out * the progress itself. A separate printing daemon periodically polls the meter to print out
* progress * progress
* *
* @param loc Current location, can be null if you are at the end of the processing unit * @param loc Current location, can be null if you are at the end of the processing unit. Must
* have size == 1 (cannot be multiple bases in size).
* @param nTotalRecordsProcessed the total number of records we've processed * @param nTotalRecordsProcessed the total number of records we've processed
*/ */
public synchronized void notifyOfProgress(final GenomeLoc loc, final long nTotalRecordsProcessed) { public synchronized void notifyOfProgress(final GenomeLoc loc, final long nTotalRecordsProcessed) {
if ( nTotalRecordsProcessed < 0 ) throw new IllegalArgumentException("nTotalRecordsProcessed must be >= 0"); if ( nTotalRecordsProcessed < 0 ) throw new IllegalArgumentException("nTotalRecordsProcessed must be >= 0");
if ( loc.size() != 1 ) throw new IllegalArgumentException("GenomeLoc must have size == 1 but got " + loc);
// weird comparison to ensure that loc == null (in unmapped reads) is keep before maxGenomeLoc == null (on startup) // weird comparison to ensure that loc == null (in unmapped reads) is keep before maxGenomeLoc == null (on startup)
this.maxGenomeLoc = loc == null ? loc : (maxGenomeLoc == null ? loc : loc.max(maxGenomeLoc)); this.maxGenomeLoc = loc == null ? loc : (maxGenomeLoc == null ? loc : loc.max(maxGenomeLoc));