throw new UnsupportedOperationException("Cannot query stream-based BAM file"); mCurrentIterator = createIndexIterator(intervals, contained); return mCurrentIterator;
throw new UnsupportedOperationException("Cannot query stream-based BAM file"); mCurrentIterator = createIndexIterator(intervals, contained); return mCurrentIterator;
throw new UnsupportedOperationException("Cannot query stream-based BAM file"); mCurrentIterator = createIndexIterator(intervals, contained); return mCurrentIterator;
throw new UnsupportedOperationException("Cannot query stream-based BAM file"); mCurrentIterator = createIndexIterator(intervals, contained); return mCurrentIterator;
} else { final QueryInterval[] queryIntervals = {new QueryInterval(referenceIndex, start, end)}; mCurrentIterator = createIndexIterator(queryIntervals, contained);
} else { final QueryInterval[] queryIntervals = {new QueryInterval(referenceIndex, start, end)}; mCurrentIterator = createIndexIterator(queryIntervals, contained);
} else { final QueryInterval[] queryIntervals = {new QueryInterval(referenceIndex, start, end)}; mCurrentIterator = createIndexIterator(queryIntervals, contained);
} else { final QueryInterval[] queryIntervals = {new QueryInterval(referenceIndex, start, end)}; mCurrentIterator = createIndexIterator(queryIntervals, contained);
if (intervals != null) { QueryInterval[] queryIntervals = BAMInputFormat.prepareQueryIntervals(intervals, header.getSequenceDictionary()); iterator = bamFileReader.createIndexIterator(queryIntervals, false, split.getIntervalFilePointers()); } else { BAMFileSpan splitSpan = new BAMFileSpan(new Chunk(virtualStart, virtualEnd));
iterator = bamFileReader.createIndexIterator(queryIntervals, false, split.getIntervalFilePointers()); } else if (boundedTraversal && split.getIntervalFilePointers() == null) {
iterator = bamFileReader.createIndexIterator(queryIntervals, false, split.getIntervalFilePointers()); } else if (boundedTraversal && split.getIntervalFilePointers() == null) {