/** * Only include reads that overlap the given intervals. Unplaced unmapped reads are not * included. * @param conf the Hadoop configuration to set properties on * @param intervals the intervals to filter by * @param <T> the {@link Locatable} type */ public static <T extends Locatable> void setIntervals(Configuration conf, List<T> intervals) { setTraversalParameters(conf, intervals, false); }
/** * Only include reads that overlap the given intervals. Unplaced unmapped reads are not * included. * @param conf the Hadoop configuration to set properties on * @param intervals the intervals to filter by * @param <T> the {@link Locatable} type */ public static <T extends Locatable> void setIntervals(Configuration conf, List<T> intervals) { setTraversalParameters(conf, intervals, false); }
private void completeSetup(boolean boundedTraversal, List<Interval> intervals, boolean traverseUnplacedUnmapped) { Configuration conf = new Configuration(); conf.set("mapred.input.dir", "file://" + input); if (boundedTraversal) { BAMInputFormat.setTraversalParameters(conf, intervals, traverseUnplacedUnmapped); } taskAttemptContext = new TaskAttemptContextImpl(conf, mock(TaskAttemptID.class)); jobContext = new JobContextImpl(conf, taskAttemptContext.getJobID()); }