updating the Tribble track loading code to use the new shared locks, updated lots of new tests, add infrastructure for the TreeInterval, and removed the old locking class.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3837 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
aaron
parent
af6b5f000e
commit
0108517b98
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@ -31,16 +31,15 @@ import org.broad.tribble.*;
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import org.broad.tribble.index.Index;
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import org.broad.tribble.index.IndexFactory;
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import org.broad.tribble.index.linear.LinearIndex;
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import org.broad.tribble.index.linear.LinearIndexCreator;
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import org.broad.tribble.source.BasicFeatureSource;
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import org.broad.tribble.vcf.NameAwareCodec;
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import org.broadinstitute.sting.gatk.refdata.tracks.TribbleTrack;
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import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrack;
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import org.broadinstitute.sting.gatk.refdata.tracks.RMDTrackCreationException;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.file.FSLock;
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import org.broadinstitute.sting.utils.classloader.PluginManager;
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import org.broadinstitute.sting.utils.StingException;
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import org.broadinstitute.sting.utils.file.FSLockWithShared;
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import java.io.File;
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import java.io.FileNotFoundException;
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@ -178,65 +177,108 @@ public class TribbleRMDTrackBuilder extends PluginManager<FeatureCodec> implemen
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// create the index file name, locking on the index file name
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File indexFile = new File(inputFile.getAbsoluteFile() + linearIndexExtension);
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FSLock lock = new FSLock(indexFile);
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FSLockWithShared lock = new FSLockWithShared(indexFile);
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// acquire a lock on the file
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boolean obtainedLock = lock.lock();
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try {
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// check to see if the index file is out of date
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if (indexFile.exists() && indexFile.canRead() && obtainedLock && indexFile.lastModified() < inputFile.lastModified()) {
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logger.warn("Tribble index file " + indexFile + " is older than the track file " + inputFile + ", deleting and regenerating");
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indexFile.delete();
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}
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// if the file exists, and we can read it, load the index from disk (i.e. wasn't deleted in the last step).
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if (indexFile.exists() && indexFile.canRead() && obtainedLock) {
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logger.info("Loading Tribble index from disk for file " + inputFile);
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Index index = IndexFactory.loadIndex(indexFile.getAbsolutePath());
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if (index.isCurrentVersion())
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return index;
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Index idx = null;
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if (indexFile.canRead())
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idx = attemptIndexFromDisk(inputFile, codec, indexFile, lock);
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logger.warn("Index file " + indexFile + " is out of date (old version), deleting and updating the index file");
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indexFile.delete();
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}
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return writeIndexToDisk(inputFile, codec, onDisk, indexFile, obtainedLock);
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// if we managed to make an index, return
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if (idx != null) return idx;
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// we couldn't read the file, or we fell out of the conditions above, continue on to making a new index
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return createNewIndex(inputFile, codec, onDisk, indexFile, lock);
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}
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/**
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* attempt to read the index from disk
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* @param inputFile the input file
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* @param codec the codec to read from
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* @param indexFile the index file itself
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* @param lock the lock file
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* @return an index, or null if we couldn't load one
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* @throws IOException if we fail for FS issues
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*/
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protected static Index attemptIndexFromDisk(File inputFile, FeatureCodec codec, File indexFile, FSLockWithShared lock) throws IOException {
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boolean locked = lock.sharedLock();
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Index idx;
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try {
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if (!locked) // can't lock file
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idx = createIndexInMemory(inputFile, codec);
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else
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idx = loadFromDisk(inputFile, indexFile);
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} finally {
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if (locked) lock.unlock();
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}
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finally {
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lock.unlock();
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return idx;
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}
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/**
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* load the index from disk, checking for out of date indexes and old versions (both of which are deleted)
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* @param inputFile the input file
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* @param indexFile the input file, plus the index extension
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* @return an Index, or null if we're unable to load
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*/
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public static Index loadFromDisk(File inputFile, File indexFile) {
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logger.info("Loading Tribble index from disk for file " + inputFile);
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Index index = IndexFactory.loadIndex(indexFile.getAbsolutePath());
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// check if the file is up-to date (filestamp and version check)
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if (index.isCurrentVersion() && indexFile.lastModified() > inputFile.lastModified())
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return index;
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else if (indexFile.lastModified() < inputFile.lastModified())
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logger.warn("Index file " + indexFile + " is out of date (index older than input file), deleting and updating the index file");
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else // we've loaded an old version of the index, we want to remove it
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logger.warn("Index file " + indexFile + " is out of date (old version), deleting and updating the index file");
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// however we got here, remove the index and return null
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boolean deleted = indexFile.delete();
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if (!deleted) logger.warn("Index file " + indexFile + " is out of date, but could not be removed; it will not be trusted (we'll try to rebuild an in-memory copy)");
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return null;
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}
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/**
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* attempt to create the index, and write it to disk
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* @param inputFile the input file
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* @param codec the codec to use
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* @param onDisk if they asked for disk storage or now
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* @param indexFile the index file location
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* @param lock the locking object
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* @return the index object
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* @throws IOException
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*/
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private static Index createNewIndex(File inputFile, FeatureCodec codec, boolean onDisk, File indexFile, FSLockWithShared lock) throws IOException {
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Index index = createIndexInMemory(inputFile, codec);
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boolean locked = false; // could we exclusive lock the file?
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try {
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locked = lock.exclusiveLock();
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if (locked) {
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logger.info("Writing Tribble index to disk for file " + inputFile);
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index.write(indexFile);
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}
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else // we can't write it to disk, just store it in memory, tell them this
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if (onDisk) logger.info("Unable to write to " + indexFile + " for the index file, creating index in memory only");
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return index;
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} finally {
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if (locked) lock.unlock();
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}
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}
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/**
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* attempt to create the index, and to disk
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* create the index in memory, given the input file and feature codec
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* @param inputFile the input file
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* @param codec the codec to use
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* @param onDisk if they asked for disk storage or now
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* @param indexFile the index file location
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* @param obtainedLock did we obtain the lock on the file?
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* @return the index object
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* @param codec the codec
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* @return a LinearIndex, given the file location
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* @throws IOException
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*/
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private static LinearIndex writeIndexToDisk(File inputFile, FeatureCodec codec, boolean onDisk, File indexFile, boolean obtainedLock) throws IOException {
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LinearIndexCreator create = new LinearIndexCreator(inputFile, codec);
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private static Index createIndexInMemory(File inputFile, FeatureCodec codec) throws IOException {
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// this can take a while, let them know what we're doing
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logger.info("Creating Tribble index in memory for file " + inputFile);
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LinearIndex index = (LinearIndex)create.createIndex(); // we don't want to write initially, so we pass in null
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// if the index doesn't exist, and we can write to the directory, and we got a lock: write to the disk
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if (indexFile.getParentFile().canWrite() &&
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(!indexFile.exists() || indexFile.canWrite()) &&
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onDisk &&
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obtainedLock) {
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logger.info("Writing Tribble index to disk for file " + inputFile);
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index.write(indexFile);
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return index;
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}
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// we can't write it to disk, just store it in memory
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else {
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// if they wanted to write, let them know we couldn't
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if (onDisk) logger.info("Unable to write to " + indexFile + " for the index file, creating index in memory only");
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return index;
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}
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return new LinearIndex(16000,inputFile.getAbsolutePath());
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}
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}
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@ -1,82 +0,0 @@
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package org.broadinstitute.sting.utils.file;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.utils.StingException;
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import java.io.File;
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import java.io.FileNotFoundException;
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import java.io.IOException;
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import java.io.RandomAccessFile;
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import java.nio.channels.FileChannel;
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import java.nio.channels.FileLock;
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/**
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* a quick implementation of a file based lock, using the Java NIO classes
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*/
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public class FSLock {
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// connect to the logger
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private static Logger logger = Logger.getLogger(FSLock.class);
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// the lock string
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private static final String lockString = ".lock";
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// the file we're attempting to lock
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private final File lockFile;
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// the file lock
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private FileLock lock = null;
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// the file channel we open
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FileChannel fc = null;
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/**
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* create a file system, given a base file to which a lock string gets appended.
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* @param baseLocation the base file location
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*/
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public FSLock(File baseLocation) {
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lockFile = new File(baseLocation.getAbsoluteFile() + lockString);
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if (lockFile != null) lockFile.deleteOnExit();
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}
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/**
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* lock the file
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*
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* @return boolean true if we obtained a lock
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*/
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public synchronized boolean lock() {
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if (lock != null) throw new IllegalStateException("Unable to lock on file " + lockFile + " there is already a lock active");
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// if the file already exists, or we can't write to the parent directory, return false
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if (lockFile.exists() || !lockFile.getParentFile().canWrite())
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return false;
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try {
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fc = new RandomAccessFile(lockFile,"rw").getChannel();
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lock = fc.tryLock();
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return lock != null && lock.isValid();
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} catch (FileNotFoundException e) {
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logger.info("Unable to create lock file (due to no file found exception), file = " + lockFile,e);
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return false;
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} catch (IOException e) {
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logger.info("Unable to create lock file (due to IO exception), file = " + lockFile,e);
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return false;
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}
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}
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/**
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* unlock the file
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*
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* note: this allows unlocking a file that failed to lock (no required user checks on null locks).
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*/
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public void unlock() {
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try {
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if (lock != null)
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lock.release();
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if (fc != null)
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fc.close();
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if (lockFile.exists())
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lockFile.delete();
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} catch (IOException e) {
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throw new StingException("Unable to create lock file named " + lockFile,e);
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}
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}
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}
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@ -24,11 +24,12 @@
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package org.broadinstitute.sting.gatk.refdata.tracks.builders;
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import org.apache.log4j.AppenderSkeleton;
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import org.apache.log4j.Logger;
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import org.apache.log4j.spi.LoggingEvent;
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import net.sf.picard.reference.IndexedFastaSequenceFile;
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import org.broad.tribble.index.Index;
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import org.broad.tribble.vcf.VCFCodec;
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import org.broadinstitute.sting.BaseTest;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.file.FSLockWithShared;
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import org.junit.Assert;
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import org.junit.Before;
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import org.junit.Test;
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@ -39,12 +40,11 @@ import java.util.Map;
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/**
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*
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* @author aaron
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*
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* Class TribbleRMDTrackBuilderUnitTest
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*
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* Testing out the builder for tribble Tracks
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* @author aaron
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* <p/>
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* Class TribbleRMDTrackBuilderUnitTest
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* <p/>
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* Testing out the builder for tribble Tracks
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*/
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public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
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private TribbleRMDTrackBuilder builder;
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@ -52,37 +52,99 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
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@Before
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public void setup() {
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builder = new TribbleRMDTrackBuilder();
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IndexedFastaSequenceFile seq = new IndexedFastaSequenceFile(new File(oneKGLocation + "reference/human_b36_both.fasta"));
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GenomeLocParser.setupRefContigOrdering(seq);
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}
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@Test
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public void testBuilder() {
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Map<String,Class> classes = builder.getAvailableTrackNamesAndTypes();
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Map<String, Class> classes = builder.getAvailableTrackNamesAndTypes();
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Assert.assertTrue(classes.size() > 0);
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}
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//@Test
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// in this test, the index exists, but is out of date.
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public void testBuilderIndexUnwriteable() {
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File vcfFile = new File(validationDataLocation + "/ROD_validation/relic.vcf");
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File vcfFile = new File(validationDataLocation + "/ROD_validation/read_only/relic.vcf");
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try {
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builder.loadIndex(vcfFile,new VCFCodec(), true);
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builder.loadIndex(vcfFile, new VCFCodec(), true);
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} catch (IOException e) {
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e.printStackTrace();
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Assert.fail("IO exception unexpected" + e.getMessage());
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}
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// make sure we didn't write the file (check that it's timestamp is within bounds)
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//System.err.println(new File(vcfFile + TribbleRMDTrackBuilder.linearIndexExtension).lastModified());
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Assert.assertTrue(Math.abs(1275597793000l - new File(vcfFile + TribbleRMDTrackBuilder.linearIndexExtension).lastModified()) < 100);
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Assert.assertTrue(Math.abs(1279591752000l - new File(vcfFile + TribbleRMDTrackBuilder.linearIndexExtension).lastModified()) < 100);
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}
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// we have a good index file, in a read-only dir. This would cause the previous version to remake the index; make
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// sure we don't do this
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@Test
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public void testDirIsLockedIndexFromDisk() {
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File vcfFile = new File(validationDataLocation + "/ROD_validation/read_only/good_index.vcf");
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File vcfFileIndex = new File(validationDataLocation + "/ROD_validation/read_only/good_index.vcf.idx");
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Index ind = null;
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try {
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ind = builder.attemptIndexFromDisk(vcfFile,new VCFCodec(),vcfFileIndex,new FSLockWithShared(vcfFile));
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} catch (IOException e) {
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Assert.fail("We weren't expecting an exception -> " + e.getMessage());
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}
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Assert.assertTrue(ind != null);
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}
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@Test
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public void testBuilderIndexDirectoryUnwritable() {
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File vcfFile = new File(validationDataLocation + "/ROD_validation/read_only/no_index.vcf.vcf");
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File vcfFileIndex = new File(validationDataLocation + "/ROD_validation/read_only/no_index.vcf.idx");
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Index ind = null;
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try {
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ind = builder.loadIndex(vcfFile, new VCFCodec(), true);
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} catch (IOException e) {
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e.printStackTrace();
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Assert.fail("IO exception unexpected" + e.getMessage());
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}
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// make sure we didn't write the file (check that it's timestamp is within bounds)
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Assert.assertTrue(!vcfFileIndex.exists());
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Assert.assertTrue(ind != null);
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}
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@Test
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public void testGenerateIndexForUnindexedFile() {
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File vcfFile = new File(validationDataLocation + "/ROD_validation/always_reindex.vcf");
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File vcfFileIndex = new File(validationDataLocation + "/ROD_validation/always_reindex.vcf.idx");
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// if we can't write to the directory, don't fault the tester, just pass
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if (!vcfFileIndex.getParentFile().canWrite()) {
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logger.warn("Unable to run test testGenerateIndexForUnindexedFile: unable to write to dir " + vcfFileIndex.getParentFile());
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return;
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}
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// clean-up our test, and previous tests that may have written the file
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vcfFileIndex.deleteOnExit();
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if (vcfFileIndex.exists()) vcfFileIndex.delete();
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try {
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builder.loadIndex(vcfFile, new VCFCodec(), true);
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} catch (IOException e) {
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e.printStackTrace();
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Assert.fail("IO exception unexpected" + e.getMessage());
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}
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// make sure we wrote the file
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Assert.assertTrue(vcfFileIndex.exists());
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}
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// test to make sure we delete the index and regenerate if it's out of date
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//@Test
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public void testBuilderIndexOutOfDate() {
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Logger logger = Logger.getLogger(TribbleRMDTrackBuilder.class);
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File vcfFile = createOutofDateIndexFile(new File(validationDataLocation + "/ROD_validation/newerTribbleTrack.vcf"));
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try {
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builder.loadIndex(vcfFile,new VCFCodec(), true);
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builder.loadIndex(vcfFile, new VCFCodec(), true);
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} catch (IOException e) {
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e.printStackTrace();
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Assert.fail("IO exception unexpected" + e.getMessage());
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@ -95,13 +157,12 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
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}
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// test to make sure we delete the index and regenerate if it's out of date
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//@Test
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// @Test
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public void testBuilderIndexGoodDate() {
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Logger logger = Logger.getLogger(TribbleRMDTrackBuilder.class);
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File vcfFile = createCorrectDateIndexFile(new File(validationDataLocation + "/ROD_validation/newerTribbleTrack.vcf"));
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Long indexTimeStamp = new File(vcfFile.getAbsolutePath() + ".idx").lastModified();
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try {
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builder.loadIndex(vcfFile,new VCFCodec(), true);
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builder.loadIndex(vcfFile, new VCFCodec(), true);
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} catch (IOException e) {
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e.printStackTrace();
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Assert.fail("IO exception unexpected" + e.getMessage());
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@ -115,14 +176,17 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
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/**
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* create a temporary file and an associated out of date index file
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*
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* @param tribbleFile the tribble file
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* @return a file pointing to the new tmp location, with out of date index
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*/
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private File createOutofDateIndexFile(File tribbleFile) {
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try {
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// first copy the tribble file to a temperary file
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File tmpFile = File.createTempFile("TribbleUnitTestFile","");
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logger.info("creating temp file " + tmpFile);
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File tmpFile = File.createTempFile("TribbleUnitTestFile", "");
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tmpFile.deleteOnExit();
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logger.info("creating temp file " + tmpFile);
|
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// create a fake index, before we copy so it's out of date
|
||||
File tmpIndex = new File(tmpFile.getAbsolutePath() + ".idx");
|
||||
tmpIndex.deleteOnExit();
|
||||
|
|
@ -131,7 +195,7 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
|
|||
Thread.sleep(2000);
|
||||
|
||||
// copy the vcf (tribble) file to the tmp file location
|
||||
copyFile(tribbleFile,tmpFile);
|
||||
copyFile(tribbleFile, tmpFile);
|
||||
|
||||
// sleep again, to make sure the timestamps are different (vcf vrs updated index file)
|
||||
Thread.sleep(2000);
|
||||
|
|
@ -148,17 +212,19 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
|
|||
|
||||
/**
|
||||
* create a temporary file and an associated out of date index file
|
||||
*
|
||||
* @param tribbleFile the tribble file
|
||||
* @return a file pointing to the new tmp location, with out of date index
|
||||
*/
|
||||
private File createCorrectDateIndexFile(File tribbleFile) {
|
||||
try {
|
||||
// first copy the tribble file to a temperary file
|
||||
File tmpFile = File.createTempFile("TribbleUnitTestFile","");
|
||||
File tmpFile = File.createTempFile("TribbleUnitTestFile", "");
|
||||
tmpFile.deleteOnExit();
|
||||
logger.info("creating temp file " + tmpFile);
|
||||
|
||||
// copy the vcf (tribble) file to the tmp file location
|
||||
copyFile(tribbleFile,tmpFile);
|
||||
copyFile(tribbleFile, tmpFile);
|
||||
|
||||
// sleep again, to make sure the timestamps are different (vcf vrs updated index file)
|
||||
Thread.sleep(2000);
|
||||
|
|
@ -168,7 +234,7 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
|
|||
tmpIndex.deleteOnExit();
|
||||
|
||||
// copy the vcf (tribble) file to the tmp file location
|
||||
copyFile(new File(tribbleFile + ".idx"),tmpIndex);
|
||||
copyFile(new File(tribbleFile + ".idx"), tmpIndex);
|
||||
|
||||
return tmpFile;
|
||||
|
||||
|
|
@ -182,6 +248,7 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
|
|||
|
||||
/**
|
||||
* copy a file, from http://www.exampledepot.com/egs/java.nio/File2File.html
|
||||
*
|
||||
* @param srFile the source file
|
||||
* @param dtFile the destination file
|
||||
*/
|
||||
|
|
@ -191,7 +258,7 @@ public class TribbleRMDTrackBuilderUnitTest extends BaseTest {
|
|||
FileChannel srcChannel = new FileInputStream(srFile).getChannel();
|
||||
|
||||
// Create channel on the destination
|
||||
FileChannel dstChannel = new FileOutputStream(dtFile).getChannel();
|
||||
FileChannel dstChannel = new FileOutputStream(dtFile).getChannel();
|
||||
|
||||
// Copy file contents from source to destination
|
||||
dstChannel.transferFrom(srcChannel, 0, srcChannel.size());
|
||||
|
|
|
|||
Loading…
Reference in New Issue