@Override
public void handle(HttpExchange t) throws IOException {
String fileId = t.getRequestURI().getPath().replaceFirst("/header/", "");
System.out.println("fileId: " + fileId);
InputStream is = new FileInputStream("C:\\Users\\vadim\\Downloads\\15496_1#45.cram");
CramHeader cramHeader = CramIO.readCramHeader(is);
t.getResponseHeaders().add(HttpHeaders.CONTENT_TYPE, "SAM_HEADER");
t.getResponseHeaders()
.add(
"CRAM_VERSION",
String.format("%d.%d", cramHeader.getMajorVersion(), cramHeader.getMinorVersion()));
t.sendResponseHeaders(200, 0);
ByteArrayOutputStream headerBodyOS = new ByteArrayOutputStream();
OutputStreamWriter w = new OutputStreamWriter(headerBodyOS);
new SAMTextHeaderCodec().encode(w, cramHeader.getSamFileHeader());
try {
w.close();
} catch (IOException e) {
throw new RuntimeException(e);
}
OutputStream os = t.getResponseBody();
os.write(headerBodyOS.toByteArray());
os.close();
}
public BaiIndexer(InputStream is, File output) throws IOException {
this.is = new CountingInputStream(is);
CramHeader cramHeader = CramIO.readCramHeader(this.is);
samFileHeader = cramHeader.getSamFileHeader();
indexer = new CRAMIndexer(output, samFileHeader);
}