inputMap.put(exId, new ByteArrayInputStream(s.external.get(exId)
.getRawContent()));
}
long time = 0;
Reader reader = f.buildReader(new DefaultBitInputStream(
new ByteArrayInputStream(s.coreBlock.getRawContent())),
inputMap, h, s.sequenceId);
List<CramRecord> records = new ArrayList<CramRecord>();
long readNanos = 0;
int prevStart = s.alignmentStart;
for (int i = 0; i < s.nofRecords; i++) {
CramRecord r = new CramRecord();
r.index = i;
try {
time = System.nanoTime();
reader.read(r);
readNanos += System.nanoTime() - time;
} catch (EOFException e) {
e.printStackTrace();
throw e;
}