From b4fda3892214df7145aed6c1ac1509dbde7039d7 Mon Sep 17 00:00:00 2001 From: Ron Levine Date: Mon, 5 Jan 2015 14:04:10 -0500 Subject: [PATCH] Use logging system instead of stderr --- .../gatk/utils/pairhmm/VectorLoglessPairHMM.java | 5 ++++- public/VectorPairHMM/src/main/c++/Sandbox.java | 9 ++++++--- .../org/broadinstitute/gatk/utils/pairhmm/PairHMM.java | 2 +- 3 files changed, 11 insertions(+), 5 deletions(-) diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java index b7f5317cf..63cce9881 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java @@ -51,6 +51,7 @@ package org.broadinstitute.gatk.utils.pairhmm; +import org.apache.log4j.Logger; import org.broadinstitute.gatk.utils.exceptions.UserException; import org.broadinstitute.gatk.utils.genotyper.ReadLikelihoods; import org.broadinstitute.gatk.utils.haplotype.Haplotype; @@ -70,6 +71,8 @@ import java.util.Map; */ public class VectorLoglessPairHMM extends JNILoglessPairHMM { + protected final static Logger logger = Logger.getLogger(VectorLoglessPairHMM.class); + //Used to copy references to byteArrays to JNI from reads protected class JNIReadDataHolderClass { public byte[] readBases = null; @@ -264,7 +267,7 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM { @Override public void close() { 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(); jniClose(); } diff --git a/public/VectorPairHMM/src/main/c++/Sandbox.java b/public/VectorPairHMM/src/main/c++/Sandbox.java index 1ec1e9056..ddfb50e59 100644 --- a/public/VectorPairHMM/src/main/c++/Sandbox.java +++ b/public/VectorPairHMM/src/main/c++/Sandbox.java @@ -25,6 +25,7 @@ package org.broadinstitute.gatk.utils.vectorpairhmm; +import org.apache.log4j.Logger; import java.util.List; import java.util.LinkedList; import java.util.Map; @@ -37,6 +38,8 @@ 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 @@ -156,7 +159,7 @@ public class Sandbox { public native void jniClose(); 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(); } @@ -170,8 +173,8 @@ public class Sandbox { } catch(FileNotFoundException e) { - System.err.println("File "+filename+" cannot be found/read"); - return; + logger.info("File "+filename + " cannot be found/read"); + return; } int idx = 0; int numReads = 0; diff --git a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java index ca9c3b192..6f7962d46 100644 --- a/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java +++ b/public/gatk-utils/src/main/java/org/broadinstitute/gatk/utils/pairhmm/PairHMM.java @@ -385,6 +385,6 @@ public abstract class PairHMM { public void close() { 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)); } }