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Use logging system instead of stderr

This commit is contained in:
Ron Levine 2015-01-05 14:04:10 -05:00
parent 64375f6341
commit b4fda38922
3 changed files with 11 additions and 5 deletions
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5
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java
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@ -51,6 +51,7 @@
package org.broadinstitute.gatk.utils.pairhmm; package org.broadinstitute.gatk.utils.pairhmm;
import org.apache.log4j.Logger;
import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods;
import org.broadinstitute.gatk.utils.haplotype.Haplotype; import org.broadinstitute.gatk.utils.haplotype.Haplotype;
@ -70,6 +71,8 @@ import java.util.Map;
*/ */
public class VectorLoglessPairHMM extends JNILoglessPairHMM { public class VectorLoglessPairHMM extends JNILoglessPairHMM {
protected final static Logger logger = Logger.getLogger(VectorLoglessPairHMM.class);
//Used to copy references to byteArrays to JNI from reads //Used to copy references to byteArrays to JNI from reads
protected class JNIReadDataHolderClass { protected class JNIReadDataHolderClass {
public byte[] readBases = null; public byte[] readBases = null;
@ -264,7 +267,7 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
@Override @Override
public void close() { public void close() {
if (doProfiling) if (doProfiling)
System.err.println("Time spent in setup for JNI call : " + (pairHMMSetupTime * 1e-9)); logger.info("Time spent in setup for JNI call : " + (pairHMMSetupTime * 1e-9));
super.close(); super.close();
jniClose(); jniClose();
} }

9
public/VectorPairHMM/src/main/c++/Sandbox.java
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@ -25,6 +25,7 @@
package org.broadinstitute.gatk.utils.vectorpairhmm; package org.broadinstitute.gatk.utils.vectorpairhmm;
import org.apache.log4j.Logger;
import java.util.List; import java.util.List;
import java.util.LinkedList; import java.util.LinkedList;
import java.util.Map; import java.util.Map;
@ -37,6 +38,8 @@ import java.io.InputStreamReader;
public class Sandbox { public class Sandbox {
protected final static Logger logger = Logger.getLogger(Sandbox.class);
private long setupTime = 0; private long setupTime = 0;
private long computeTime = 0; private long computeTime = 0;
//Used to copy references to byteArrays to JNI from reads //Used to copy references to byteArrays to JNI from reads
@ -156,7 +159,7 @@ public class Sandbox {
public native void jniClose(); public native void jniClose();
public void close() public void close()
{ {
System.err.println("Time spent in setup for JNI call : "+(setupTime*1e-9)+" compute time : "+(computeTime*1e-9)); logger.info("Time spent in setup for JNI call : "+(setupTime*1e-9)+" compute time : "+(computeTime*1e-9));
jniClose(); jniClose();
} }
@ -170,8 +173,8 @@ public class Sandbox {
} }
catch(FileNotFoundException e) catch(FileNotFoundException e)
{ {
System.err.println("File "+filename+" cannot be found/read"); logger.info("File "+filename + " cannot be found/read");
return; return;
} }
int idx = 0; int idx = 0;
int numReads = 0; int numReads = 0;

2
public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java
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@ -385,6 +385,6 @@ public abstract class PairHMM {
public void close() public void close()
{ {
if(doProfiling) if(doProfiling)
System.err.println("Total compute time in PairHMM computeLikelihoods() : "+(pairHMMComputeTime*1e-9)); logger.info("Total compute time in PairHMM computeLikelihoods() : "+(pairHMMComputeTime*1e-9));
} }
} }