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Print to logger not to System.out in CachingIndexFastaSequenceFile when profiling cache performance

This commit is contained in:
Mark DePristo 2012-08-17 11:41:07 -04:00
parent be0f8beebb
commit daa26cc64e
1 changed files with 3 additions and 1 deletions
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4
public/java/src/org/broadinstitute/sting/utils/fasta/CachingIndexedFastaSequenceFile.java
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@ -41,6 +41,8 @@ import java.util.Arrays;
* Thread-safe! Uses a lock object to protect write and access to the cache.
*/
public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile {
protected static final org.apache.log4j.Logger logger = org.apache.log4j.Logger.getLogger(CachingIndexedFastaSequenceFile.class);
/** global enable flag */
private static final boolean USE_CACHE = true;
@ -125,7 +127,7 @@ public class CachingIndexedFastaSequenceFile extends IndexedFastaSequenceFile {
public void printEfficiency() {
// comment out to disable tracking
if ( (cacheHits + cacheMisses) % PRINT_FREQUENCY == 0 ) {
System.out.printf("### CachingIndexedFastaReader: hits=%d misses=%d efficiency %.6f%%%n", cacheHits, cacheMisses, calcEfficiency());
logger.info(String.format("### CachingIndexedFastaReader: hits=%d misses=%d efficiency %.6f%%%n", cacheHits, cacheMisses, calcEfficiency()));
}
}