Format format = new FormatFactory().createFormat(definition);
SAMRecord samRecord = null;
CramHeader cramHeader = createCramHeader(reader.getFileHeader());
ByteArrayOutputStream hBaos= new ByteArrayOutputStream() ;
Container hC = new Container() ;
Block hBlock = new Block() ;
hBlock.contentId=0;
hBlock.contentType=0;
hBlock.method = CompressionMethod.GZIP.byteValue() ;
hC.blocks = new Block[]{hBlock} ;
hC.containers= new Container[0] ;
CramHeaderIO.write(cramHeader, hBaos) ;
hBlock.data = hBaos.toByteArray() ;
format.writeContainer(hC, hBaos) ;
System.out.println("Header size: " + hBaos.size());
for (int b = 0; b < maxRecords; b+=recordsPerBlock) {
bases = 0 ;
size = 0 ;
for (int i = 0; i < recordsPerBlock; i++) {
samRecord = iterator.next();
a.addSAMRecord(samRecord);
bases += samRecord.getReadLength();
}
for (int i = 0; i < recordsPerBlock; i++) {
while ((samRecord = a.nextSAMRecord()) != null) {
CramRecord cramRecord = scFactory.createCramRecord(samRecord);
records.add(cramRecord);
setPairingInformation(cramRecord, samRecord, a.distanceToNextFragment());
}
while ((samRecord = a.fetchNextSAMRecord()) != null) {
CramRecord cramRecord = scFactory.createCramRecord(samRecord);
records.add(cramRecord);
setPairingInformation(cramRecord, samRecord, a.distanceToNextFragment());
}
}
Container container = new Coder(recordsPerSlice).writeRecords(cramHeader, records, provider);
ByteArrayOutputStream baos = new ByteArrayOutputStream();
long time1 = System.nanoTime();
format.writeContainer(container, baos);
long time2 = System.nanoTime();
System.out.printf("Container written: bytes=%d in %.2f ms.\n", baos.size(), (time2 - time1) / 1000000f);
size += baos.size();
records.clear();
System.out.printf("Total records: %d, bases=%d, bytes=%d, b/b=%.2f\n", counter, bases, size, 8f * size
/ bases);
time1 = System.nanoTime();
Container c = format.readContainer(new ByteArrayInputStream(baos.toByteArray()));
time2 = System.nanoTime();
System.out.printf("Container read in %.2f ms.\n", (time2 - time1) / 1000000f);
time1 = System.nanoTime();
List<CramRecord> readRecords = new Coder(recordsPerSlice).readRecords(c, cramHeader, provider);