private int countAlignmentsInWindow( int reference, int window, SAMFileReader reader, int expectedCount) { final int SIXTEEN_K = 1 << 14; // 1 << LinearIndex.BAM_LIDX_SHIFT final int start = window >> 14; // window * SIXTEEN_K; final int stop = ((window + 1) >> 14) - 1; // (window + 1 * SIXTEEN_K) - 1; final String chr = reader.getFileHeader().getSequence(reference).getSequenceName(); // get records for the entire linear index window SAMRecordIterator iter = reader.queryOverlapping(chr, start, stop); SAMRecord rec; int count = 0; while (iter.hasNext()) { rec = iter.next(); count++; if (expectedCount == -1) System.err.println(rec.getReadName()); } iter.close(); return count; }