Java SortingCollection.doneAdding方法代码示例

import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
private void runSingle(final FastqReader r1,final FastqWriter w1) throws IOException
{
long nReads=0;
final  SortingCollection<OneRead> sorting= SortingCollection.newInstance(
		OneRead.class,
		new OneReadCodec(),
		new OneReadCompare(),
		this.writingSortingCollection.getMaxRecordsInRam(),
		this.writingSortingCollection.getTmpPaths()
		);
sorting.setDestructiveIteration(true);
while(r1.hasNext())
	{
	final OneRead r=new OneRead();
	r.random=this.random.nextLong();
	r.index=nReads;
	r.first=r1.next();
	
	if((++nReads)%this.writingSortingCollection.getMaxRecordsInRam()==0)
		{
		LOG.info("Read "+nReads+" reads");
		}

	
	sorting.add(r);
	}
sorting.doneAdding();

final CloseableIterator<OneRead> iter=sorting.iterator();
while(iter.hasNext())
	{
	final OneRead p=iter.next();
	w1.write(p.first);
	}

	
CloserUtil.close(iter);
sorting.cleanup();
}
 

import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
@Override
public int doWork(final List<String> args) {
	if(this.count<-1L) // -1 == infinite
		{
		LOG.error("Bad count:"+count);
		return -1;
		}
	SamReader samReader=null;
	SAMRecordIterator iter=null;
	SAMFileWriter samWriter=null;
	Random random=new Random();
	CloseableIterator<RandSamRecord> iter2=null;
	try
		{
		
		samReader = super.openSamReader(oneFileOrNull(args));
		
		final SAMFileHeader header=samReader.getFileHeader().clone();
					
		header.setSortOrder(SortOrder.unsorted);
		header.addComment("Processed with "+getProgramName()+" : "+getProgramCommandLine());
		
		samWriter = writingBamArgs.openSAMFileWriter(outputFile, header, true);
		
		iter=samReader.iterator();
		SAMSequenceDictionaryProgress progress=new SAMSequenceDictionaryProgress(samReader.getFileHeader().getSequenceDictionary());
		
		SortingCollection<RandSamRecord> sorter=SortingCollection.newInstance(
				RandSamRecord.class,
				new RandSamRecordCodec(header),
				new RandSamRecordComparator(), 
				this.writingSortingCollection.getMaxRecordsInRam(),
				this.writingSortingCollection.getTmpPaths()
				);
		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)
		{
		LOG.error(e);
		return -1;
		}
	finally
		{
		CloserUtil.close(iter);
		CloserUtil.close(iter2);
		CloserUtil.close(samReader);
		CloserUtil.close(samWriter);
		}
	return 0;
	}
 

import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
@Override
public int doWork(List<String> args) {
	SamReader in=null;
	SAMFileWriter out=null;
	SAMRecordIterator iter=null;
	CloseableIterator<SAMRecord> iter2=null;
	SortingCollection<SAMRecord> sorter=null;
	try
		{
		in  = openSamReader(oneFileOrNull(args));
		final SAMFileHeader header= in.getFileHeader();
		
		final BAMRecordCodec bamRecordCodec=new BAMRecordCodec(header);
		final RefNameComparator refNameComparator=new RefNameComparator();
		sorter =SortingCollection.newInstance(
				SAMRecord.class,
				bamRecordCodec,
				refNameComparator,
				this.writingSortingCollection.getMaxRecordsInRam(),
				this.writingSortingCollection.getTmpPaths()
				);
		sorter.setDestructiveIteration(true);
		
		final SAMSequenceDictionaryProgress progress=new SAMSequenceDictionaryProgress(header);
		iter = in.iterator();
		while(iter.hasNext())
			{
			sorter.add( progress.watch(iter.next()));
			}
		in.close();in=null;
		sorter.doneAdding();
		
		final SAMFileHeader header2=header.clone();
		header2.addComment(getProgramName()+" "+getVersion()+" "+getProgramCommandLine());
		header2.setSortOrder(SortOrder.unsorted);
		out = this.writingBamArgs.openSAMFileWriter(outputFile,header2, true);
		iter2 = sorter.iterator();
		while(iter2.hasNext())
			{
			out.addAlignment(iter2.next());
			}
		out.close();out=null;
		sorter.cleanup();
		progress.finish();
		LOG.info("done");
		return RETURN_OK;
		}
	catch(Exception err)
		{
		LOG.error(err);
		return -1;
		}
	finally
		{
		CloserUtil.close(iter2);
		CloserUtil.close(iter);
		CloserUtil.close(out);
		CloserUtil.close(in);
		}
	}
 

import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
protected int sortvcf(BufferedReader in) throws IOException 
  	{
if(this.refdict!=null) {
	LOG.info("load dict from "+this.refdict);
	this.dict = SAMSequenceDictionaryExtractor.extractDictionary(this.refdict);
	if(this.dict==null) {
		LOG.error("cannot find sam sequence dictionary from "+refdict);
	}
}

final VCFUtils.CodecAndHeader cah =VCFUtils.parseHeader(in);
  	final VCFHeader h2=new  VCFHeader(cah.header);
  	if(this.dict!=null)
  		{
  		h2.setSequenceDictionary(this.dict);
  		}
  	else
  		{
  		this.dict= h2.getSequenceDictionary();
  		if(this.dict==null)
  			{
  			LOG.error("No internal sequence dictionay found in input");
  			return -1;
  			}
  		}
  	
  	addMetaData(h2);

if(this.dict.isEmpty())
	{
	LOG.warn("SEQUENCE DICTIONARY IS EMPTY/NULL");
	}

  	CloseableIterator<ChromPosLine> iter=null;
  	SortingCollection<ChromPosLine> array=null;
  	VariantContextWriter w =null;
  	try {
	array= SortingCollection.newInstance(
			ChromPosLine.class,
			new VariantCodec(),
			new VariantComparator(),
			this.writingSortingCollection.getMaxRecordsInRam(),
			this.writingSortingCollection.getTmpPaths()
			);
	array.setDestructiveIteration(true);
	final SAMSequenceDictionaryProgress progress=new SAMSequenceDictionaryProgress(this.dict);
	String line;
	while((line=in.readLine())!=null)
		{
		final ChromPosLine cpl=new ChromPosLine(line);
		progress.watch(cpl.tid,cpl.pos);
		array.add(cpl);
		}
	array.doneAdding();
	progress.finish();
	
	w = super.openVariantContextWriter(outputFile);
	w.writeHeader(h2);
	
	iter=array.iterator();
	while(iter.hasNext())
		{
		w.add(cah.codec.decode(iter.next().line));
		if(w.checkError()) break;
		}
	return RETURN_OK;
	}
  	catch (Exception e)
  		{
	LOG.error(e);
	return -1;
	}
  	finally
   	{
  		CloserUtil.close(w);
   	CloserUtil.close(iter);
   	if(array!=null) array.cleanup();
   	}
  	
  	}