/** * Prepare to iterate through SAMRecords that match the intersection of the given intervals and chunk boundaries. * @param intervals the intervals to restrict reads to * @param contained if <code>true</code>, return records that are strictly * contained in the intervals, otherwise return records that overlap * @param filePointers file pointer pairs corresponding to chunk boundaries for the * intervals */ public CloseableIterator<SAMRecord> createIndexIterator(final QueryInterval[] intervals, final boolean contained, final long[] filePointers) { return new CRAMIntervalIterator(intervals, contained, filePointers); }
/** * Prepare to iterate through SAMRecords that match the intersection of the given intervals and chunk boundaries. * @param intervals the intervals to restrict reads to * @param contained if <code>true</code>, return records that are strictly * contained in the intervals, otherwise return records that overlap * @param filePointers file pointer pairs corresponding to chunk boundaries for the * intervals */ public CloseableIterator<SAMRecord> createIndexIterator(final QueryInterval[] intervals, final boolean contained, final long[] filePointers) { return new CRAMIntervalIterator(intervals, contained, filePointers); }
@Override public CloseableIterator<SAMRecord> queryAlignmentStart(final String sequence, final int start) { final SAMFileHeader fileHeader = getFileHeader(); final int referenceIndex = fileHeader.getSequenceIndex(sequence); return new CRAMIntervalIterator(new QueryInterval[]{new QueryInterval(referenceIndex, start, -1)}, true); }
@Override public CloseableIterator<SAMRecord> query(final QueryInterval[] intervals, final boolean contained) { return new CRAMIntervalIterator(intervals, contained); }
@Override public CloseableIterator<SAMRecord> queryAlignmentStart(final String sequence, final int start) { final SAMFileHeader fileHeader = getFileHeader(); final int referenceIndex = fileHeader.getSequenceIndex(sequence); return new CRAMIntervalIterator(new QueryInterval[]{new QueryInterval(referenceIndex, start, -1)}, true); }
@Override public CloseableIterator<SAMRecord> query(final QueryInterval[] intervals, final boolean contained) { return new CRAMIntervalIterator(intervals, contained); }