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;
}
