@Override
public void close() {
try {
in.close();
} catch (final IOException e) {
throw new RuntimeIOException(e);
}
}
public static void main(String[] args) throws IOException {
final GenericOptionsParser parser;
try {
parser = new GenericOptionsParser(args);
// This should be IOException but Hadoop 0.20.2 doesn't throw it...
} catch (Exception e) {
System.err.printf("Error in Hadoop arguments: %s\n", e.getMessage());
System.exit(1);
// Hooray for javac
return;
}
args = parser.getRemainingArgs();
// final Configuration conf = ContextUtil.getConfiguration(parser);
final Configuration conf = parser.getConfiguration();
long beg = 0;
if (args.length < 2 || args.length > 3) {
System.err.println("Usage: BAMSplitGuesser path-or-uri header-path-or-uri [beg]");
System.exit(2);
}
try {
if (args.length > 2) beg = Long.decode(args[2]);
} catch (NumberFormatException e) {
System.err.println("Invalid beg offset.");
if (e.getMessage() != null) System.err.println(e.getMessage());
System.exit(2);
}
SeekableStream ss = WrapSeekable.openPath(conf, new Path(args[0]));
SeekableStream hs = WrapSeekable.openPath(conf, new Path(args[1]));
final long end = beg + MAX_BYTES_READ;
System.out.printf(
"Will look for a BGZF block within: [%1$#x,%2$#x) = [%1$d,%2$d)\n"
+ "Will then verify BAM data within: [%1$#x,%3$#x) = [%1$d,%3$d)\n",
beg, beg + 0xffff, end);
final long g = new BAMSplitGuesser(ss, hs, conf).guessNextBAMRecordStart(beg, end);
ss.close();
if (g == end) {
System.out.println("Didn't find any acceptable BAM record in any BGZF block.");
System.exit(1);
}
System.out.printf(
"Accepted BGZF block at offset %1$#x (%1$d).\n"
+ "Accepted BAM record at offset %2$#x (%2$d) therein.\n",
g >> 16, g & 0xffff);
}