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Do not use logger, write to stderr, could not get the correct logger dependency in pom.xml

This commit is contained in:
Ron Levine 2015-01-06 10:32:11 -05:00
parent 26c46ae05e
commit 7d58544f17
1 changed files with 2 additions and 5 deletions
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7
public/VectorPairHMM/src/main/c++/Sandbox.java
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@ -25,7 +25,6 @@
package org.broadinstitute.gatk.utils.vectorpairhmm;
import org.apache.log4j.Logger;
import java.util.List;
import java.util.LinkedList;
import java.util.Map;
@ -38,8 +37,6 @@ import java.io.InputStreamReader;
public class Sandbox {
protected final static Logger logger = Logger.getLogger(Sandbox.class);
private long setupTime = 0;
private long computeTime = 0;
//Used to copy references to byteArrays to JNI from reads
@ -159,7 +156,7 @@ public class Sandbox {
public native void jniClose();
public void close()
{
logger.info("Time spent in setup for JNI call : "+(setupTime*1e-9)+" compute time : "+(computeTime*1e-9));
System.err.println("Time spent in setup for JNI call : " + (setupTime * 1e-9) + " compute time : " + (computeTime * 1e-9));
jniClose();
}
@ -173,7 +170,7 @@ public class Sandbox {
}
catch(FileNotFoundException e)
{
logger.error("File "+filename + " cannot be found/read");
System.err.println("File "+filename + " cannot be found/read");
return;
}
int idx = 0;