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GATKPerformanceOverTime script update 

-- Automatic detection of most recent version of GATK release (just tell the script now to use 1.2, 1.3, and 1.4)
-- Uses 1.4 now
-- By default we do 9 runs of each non-parallel test
-- In PathUtils added convenience utility to find most recent release GATK jar with a specific release number
This commit is contained in:
Mark DePristo 2012-01-02 09:58:46 -05:00
parent a837970ea2
commit d05f0c2318
1 changed files with 51 additions and 2 deletions
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53
public/java/src/org/broadinstitute/sting/utils/PathUtils.java
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@ -1,10 +1,14 @@
package org.broadinstitute.sting.utils;
import org.apache.commons.io.comparator.LastModifiedFileComparator;
import org.apache.log4j.Logger;
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import java.io.File;
import java.io.FilenameFilter;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.List;
/**
@ -17,6 +21,8 @@ import java.util.List;
* A set of static utility methods for common operations on paths.
*/
public class PathUtils {
private static Logger logger = Logger.getLogger(PathUtils.class);
/**
* Constructor access disallowed...static utility methods only!
*/
@ -36,7 +42,7 @@ public class PathUtils {
List<String> filesInPath = new ArrayList<String>();
FilenameFilter filter = new OrFilenameFilter(new DirectoryFilter(),
new ExtensionFilter(extension));
new ExtensionFilter(extension));
File[] contents = basePath.listFiles( filter );
for (File content : contents) {
String relativeFileName = relativePrefix.trim().length() != 0 ?
@ -118,4 +124,47 @@ public class PathUtils {
}
}
}
/**
* Walk over the GATK released directories to find the most recent JAR files corresponding
* to the version prefix. For example, providing input "1.2" will
* return the full path to the most recent GenomeAnalysisTK.jar in the GATK_RELEASE_DIR
* in directories that match gatkReleaseDir/GenomeAnalysisTK-1.2*
*
* @param gatkReleaseDir Path to directory containing GATK release binaries (e.g., /humgen/gsa-hpprojects/GATK/bin/)
* @param releaseVersionNumber Desired GATK version number (e.g., 1.2)
* @return A file pointing to the most recent GATK file in the release directory with GATK release number
*/
public static File findMostRecentGATKVersion(final File gatkReleaseDir, final String releaseVersionNumber) {
final String versionString = "GenomeAnalysisTK-" + releaseVersionNumber;
final List<File> gatkJars = new ArrayList<File>();
for ( final String path : gatkReleaseDir.list(new isGATKVersion(versionString)) ) {
gatkJars.add(new File(gatkReleaseDir.getAbsolutePath() + "/" + path + "/GenomeAnalysisTK.jar"));
}
if ( gatkJars.isEmpty() )
return null;
else {
Collections.sort(gatkJars, LastModifiedFileComparator.LASTMODIFIED_REVERSE);
//for ( File jar : gatkJars ) logger.info(String.format("%s => %d", jar, jar.lastModified()));
final File last = gatkJars.get(0);
logger.debug(String.format("findMostRecentGATKVersion: Found %d jars for %s, keeping last one %s",
gatkJars.size(), releaseVersionNumber, last));
return last;
}
}
private final static class isGATKVersion implements FilenameFilter {
private final String versionString;
private isGATKVersion(final String versionString) {
this.versionString = versionString;
}
@Override
public boolean accept(final File file, final String s) {
return s.contains(versionString);
}
}
}