List<Interval> intervals = BAMInputFormat.getIntervals(conf); if (intervals != null) { QueryInterval[] queryIntervals = BAMInputFormat.prepareQueryIntervals(intervals, header.getSequenceDictionary());
private List<InputSplit> filterByInterval(List<InputSplit> splits, Configuration conf) throws IOException { List<Interval> intervals = getIntervals(conf); if (intervals == null) { return splits;
if (boundedTraversal && split.getIntervalFilePointers() != null) { List<Interval> intervals = BAMInputFormat.getIntervals(conf); QueryInterval[] queryIntervals = BAMInputFormat.prepareQueryIntervals(intervals, header.getSequenceDictionary()); iterator = bamFileReader.createIndexIterator(queryIntervals, false, split.getIntervalFilePointers());
if (boundedTraversal && split.getIntervalFilePointers() != null) { List<Interval> intervals = BAMInputFormat.getIntervals(conf); QueryInterval[] queryIntervals = BAMInputFormat.prepareQueryIntervals(intervals, header.getSequenceDictionary()); iterator = bamFileReader.createIndexIterator(queryIntervals, false, split.getIntervalFilePointers());
.setUseAsyncIo(false); List<Interval> intervals = getIntervals(conf);
.setUseAsyncIo(false); List<Interval> intervals = getIntervals(conf);