private Collection<Throwable> execute_bam(String source) throws IOException {
SamReader in = null;
SAMRecordIterator iter = null;
try {
SamReaderFactory srf =
SamReaderFactory.makeDefault().validationStringency(ValidationStringency.SILENT);
if (source == null) {
in = srf.open(SamInputResource.of(stdin()));
} else {
in = srf.open(SamInputResource.of(source));
}
iter = in.iterator();
bindings.put("header", in.getFileHeader());
bindings.put("iter", iter);
bindings.put("format", "sam");
this.script.eval(bindings);
return RETURN_OK;
} catch (Exception e) {
LOG.error(e);
return wrapException(e);
} finally {
CloserUtil.close(in);
CloserUtil.close(iter);
bindings.remove("header");
bindings.remove("iter");
bindings.remove("format");
}
}
public CloseableIterator<PicardAlignment> iterator() {
try {
if (reader == null) {
InputStream is = HttpUtils.getInstance().openConnectionStream(url);
reader = new SAMFileReader(new BufferedInputStream(is));
}
return new WrappedIterator(reader.iterator());
} catch (IOException e) {
log.error("Error creating iterator", e);
throw new RuntimeException(e);
}
}
@Exec
public void exec() throws IOException, CommandArgumentException {
if (filename == null) {
throw new CommandArgumentException("You must specify an input BAM filename!");
}
SamReaderFactory readerFactory = SamReaderFactory.makeDefault();
if (lenient) {
readerFactory.validationStringency(ValidationStringency.LENIENT);
} else if (silent) {
readerFactory.validationStringency(ValidationStringency.SILENT);
}
SamReader reader = null;
String name;
FileChannel channel = null;
if (filename.equals("-")) {
reader = readerFactory.open(SamInputResource.of(System.in));
name = "<stdin>";
} else {
File f = new File(filename);
FileInputStream fis = new FileInputStream(f);
channel = fis.getChannel();
reader = readerFactory.open(SamInputResource.of(fis));
name = f.getName();
}
Iterator<SAMRecord> it =
ProgressUtils.getIterator(
name,
reader.iterator(),
(channel == null) ? null : new FileChannelStats(channel),
new ProgressMessage<SAMRecord>() {
long i = 0;
@Override
public String msg(SAMRecord current) {
i++;
return i + " " + current.getReadName();
}
},
new CloseableFinalizer<SAMRecord>());
long i = 0;
while (it.hasNext()) {
i++;
it.next();
}
reader.close();
System.err.println("Successfully read: " + i + " records.");
}
@Override
public int doWork(String[] args) {
boolean compressed = false;
int maxRecordsInRAM = 100000;
long count = -1L;
File fileout = null;
com.github.lindenb.jvarkit.util.cli.GetOpt opt =
new com.github.lindenb.jvarkit.util.cli.GetOpt();
int c;
while ((c = opt.getopt(args, getGetOptDefault() + "o:n:N:T:b")) != -1) {
switch (c) {
case 'b':
compressed = true;
break;
case 'N':
maxRecordsInRAM = Integer.parseInt(opt.getOptArg());
break;
case 'n':
count = Long.parseLong(opt.getOptArg());
break;
case 'o':
fileout = new File(opt.getOptArg());
break;
case 'T':
this.addTmpDirectory(new File(opt.getOptArg()));
break;
default:
{
switch (handleOtherOptions(c, opt, null)) {
case EXIT_FAILURE:
return -1;
case EXIT_SUCCESS:
return 0;
default:
break;
}
}
}
}
if (count < -1L) // -1 == infinite
{
error("Bad count:" + count);
return -1;
}
SamReader samReader = null;
SAMRecordIterator iter = null;
SAMFileWriter samWriter = null;
Random random = new Random();
CloseableIterator<RandSamRecord> iter2 = null;
try {
SamFileReaderFactory.setDefaultValidationStringency(ValidationStringency.SILENT);
if (opt.getOptInd() == args.length) {
info("Reading from stdin");
samReader = SamFileReaderFactory.mewInstance().openStdin();
} else if (opt.getOptInd() + 1 == args.length) {
File filename = new File(args[opt.getOptInd()]);
info("Reading from " + filename);
samReader = SamFileReaderFactory.mewInstance().open(filename);
} else {
error("Illegal number of arguments.");
return -1;
}
SAMFileHeader header = samReader.getFileHeader();
header = header.clone();
header.setSortOrder(SortOrder.unsorted);
header.addComment("Processed with " + getProgramName() + " : " + getProgramCommandLine());
SAMFileWriterFactory sfw = new SAMFileWriterFactory();
sfw.setCreateIndex(false);
sfw.setCreateMd5File(false);
if (fileout == null) {
if (compressed) {
samWriter = sfw.makeBAMWriter(header, true, System.out);
} else {
samWriter = sfw.makeSAMWriter(header, true, System.out);
}
} else {
samWriter = sfw.makeSAMOrBAMWriter(header, true, fileout);
this.addTmpDirectory(fileout);
}
iter = samReader.iterator();
SAMSequenceDictionaryProgress progress =
new SAMSequenceDictionaryProgress(samReader.getFileHeader().getSequenceDictionary());
SortingCollection<RandSamRecord> sorter =
SortingCollection.newInstance(
RandSamRecord.class,
new RandSamRecordCodec(header),
new RandSamRecordComparator(),
maxRecordsInRAM,
getTmpDirectories());
sorter.setDestructiveIteration(true);
while (iter.hasNext()) {
RandSamRecord r = new RandSamRecord();
r.rand_index = random.nextInt();
r.samRecord = progress.watch(iter.next());
sorter.add(r);
}
iter.close();
iter = null;
sorter.doneAdding();
iter2 = sorter.iterator();
if (count == -1) {
while (iter2.hasNext()) {
samWriter.addAlignment(iter2.next().samRecord);
}
} else {
while (iter2.hasNext() && count > 0) {
samWriter.addAlignment(iter2.next().samRecord);
count--;
}
}
iter2.close();
iter2 = null;
sorter.cleanup();
progress.finish();
} catch (Exception e) {
error(e);
return -1;
} finally {
CloserUtil.close(iter);
CloserUtil.close(iter2);
CloserUtil.close(samReader);
CloserUtil.close(samWriter);
}
return 0;
}
private BAMProcessorImplDict(File in) {
reader = SamReaderFactory.makeDefault().open(in);
iterator = reader.iterator();
queue = new LinkedList<SAMRecord>();
}