diff --git a/public/java/src/org/broadinstitute/sting/utils/PathUtils.java b/public/java/src/org/broadinstitute/sting/utils/PathUtils.java index 822d04dfd..db655d25c 100755 --- a/public/java/src/org/broadinstitute/sting/utils/PathUtils.java +++ b/public/java/src/org/broadinstitute/sting/utils/PathUtils.java @@ -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 filesInPath = new ArrayList(); 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 gatkJars = new ArrayList(); + 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); + } + } +} \ No newline at end of file