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Added run-time information to log output 

Also updated copyright date
This commit is contained in:
Yossi Farjoun 2016-03-10 09:53:26 -05:00 committed by Geraldine Van der Auwera
parent 71d816d8f5
commit b471884d97
1 changed files with 13 additions and 1 deletions
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14
public/gatk-engine/src/main/java/org/broadinstitute/gatk/engine/CommandLineGATK.java
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@ -26,6 +26,7 @@
package org.broadinstitute.gatk.engine; package org.broadinstitute.gatk.engine;
import htsjdk.samtools.SAMException; import htsjdk.samtools.SAMException;
import htsjdk.samtools.util.zip.DeflaterFactory;
import htsjdk.tribble.TribbleException; import htsjdk.tribble.TribbleException;
import org.broadinstitute.gatk.utils.commandline.Argument; import org.broadinstitute.gatk.utils.commandline.Argument;
import org.broadinstitute.gatk.utils.commandline.ArgumentCollection; import org.broadinstitute.gatk.utils.commandline.ArgumentCollection;
@ -38,6 +39,7 @@ import org.broadinstitute.gatk.utils.exceptions.UserException;
import org.broadinstitute.gatk.utils.help.*; import org.broadinstitute.gatk.utils.help.*;
import org.broadinstitute.gatk.utils.text.TextFormattingUtils; import org.broadinstitute.gatk.utils.text.TextFormattingUtils;
import java.net.InetAddress;
import java.util.*; import java.util.*;
/** /**
@ -169,8 +171,18 @@ public class CommandLineGATK extends CommandLineExecutable {
public static List<String> createApplicationHeader() { public static List<String> createApplicationHeader() {
List<String> header = new ArrayList<String>(); List<String> header = new ArrayList<String>();
header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",getVersionNumber(), getBuildTime())); header.add(String.format("The Genome Analysis Toolkit (GATK) v%s, Compiled %s",getVersionNumber(), getBuildTime()));
header.add("Copyright (c) 2010 The Broad Institute"); header.add("Copyright (c) 2010-2016 The Broad Institute");
header.add("For support and documentation go to " + HelpConstants.BASE_GATK_URL); header.add("For support and documentation go to " + HelpConstants.BASE_GATK_URL);
try {
header.add("[" + new Date() + "] Executing on " +
System.getProperty("os.name") + " " + System.getProperty("os.version") +
" " + System.getProperty("os.arch"));
header.add( System.getProperty("java.vm.name") +
" " + System.getProperty("java.runtime.version") +
" " + (DeflaterFactory.usingIntelDeflater()? "IntelDeflater": "JdkDeflater"));
}
catch (Exception e) { /* Unpossible! */ }
return header; return header;
} }