QueryInterval[] queryIntervals = BAMInputFormat.prepareQueryIntervals(intervals, header.getSequenceDictionary()); iterator = bamFileReader.createIndexIterator(queryIntervals, false, split.getIntervalFilePointers()); } else {
SAMSequenceDictionary dict = header.getSequenceDictionary(); BAMIndex idx = samReader.indexing().getIndex(); QueryInterval[] queryIntervals = prepareQueryIntervals(intervals, dict); fileToSpan.put(bamFile, BAMFileReader.getFileSpan(queryIntervals, idx));
QueryInterval[] queryIntervals = BAMInputFormat.prepareQueryIntervals(intervals, header.getSequenceDictionary()); iterator = bamFileReader.createIndexIterator(queryIntervals, false, split.getIntervalFilePointers()); } else if (boundedTraversal && split.getIntervalFilePointers() == null) {
QueryInterval[] queryIntervals = BAMInputFormat.prepareQueryIntervals(intervals, header.getSequenceDictionary()); iterator = bamFileReader.createIndexIterator(queryIntervals, false, split.getIntervalFilePointers()); } else if (boundedTraversal && split.getIntervalFilePointers() == null) {
QueryInterval[] queryIntervals = prepareQueryIntervals(intervals, dict); fileToSpan.put(bamFile, BAMFileReader.getFileSpan(queryIntervals, idx));
QueryInterval[] queryIntervals = prepareQueryIntervals(intervals, dict); fileToSpan.put(bamFile, BAMFileReader.getFileSpan(queryIntervals, idx));