Examples of org.broadinstitute.gatk.utils.file.FSLockWithShared$LockAcquisitionTask

Package org.broadinstitute.gatk.utils.file

Examples of org.broadinstitute.gatk.utils.file.FSLockWithShared$LockAcquisitionTask

org.broadinstitute.gatk.utils.file.FSLockWithShared
Background task that attempts to acquire a lock of the specified type, and returns a boolean indicating success/failure. Uses a non-blocking tryLock() call that should return immediately (but may get stuck if there's a problem with the OS locking daemon).

                    validateAndUpdateIndexSequenceDictionary(inputFile, index, dict);


                    if ( ! disableAutoIndexCreation ) {
                        File indexFile = Tribble.indexFile(inputFile);
                        try { // re-write the index
                            writeIndexToDisk(index,indexFile,new FSLockWithShared(indexFile));
                        } catch (IOException e) {
                            logger.warn("Unable to update index with the sequence dictionary for file " + indexFile + "; this will not affect your run of the GATK");
                        }
                    }

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     * @return a linear index for the specified type
     * @throws IOException if we cannot write the index file
     */
    public synchronized Index loadIndex( final File inputFile, final FeatureCodec codec) throws IOException {
        final File indexFile = Tribble.indexFile(inputFile);
        final FSLockWithShared lock = new FSLockWithShared(indexFile);
        Index idx = null;


        // If the index file exists and is readable, attempt to load it from disk. We'll get null back
        // if a problem was discovered with the index file when it was inspected, and we'll get an
        // in-memory index back in the case where the index file could not be locked.

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