本文整理汇总了Java中htsjdk.samtools.util.SortingCollection.doneAdding方法的典型用法代码示例。如果您正苦于以下问题:Java SortingCollection.doneAdding方法的具体用法?Java SortingCollection.doneAdding怎么用?Java SortingCollection.doneAdding使用的例子?那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类htsjdk.samtools.util.SortingCollection
的用法示例。
在下文中一共展示了SortingCollection.doneAdding方法的4个代码示例,这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞,您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: runSingle
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();
}
示例2: doWork
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;
}
示例3: doWork
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);
}
}
示例4: sortvcf
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();
}
}