本文整理汇总了Java中htsjdk.samtools.util.SortingCollection.newInstance方法的典型用法代码示例。如果您正苦于以下问题:Java SortingCollection.newInstance方法的具体用法?Java SortingCollection.newInstance怎么用?Java SortingCollection.newInstance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.newInstance方法的14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: RevertSamSorter
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
RevertSamSorter(
final boolean outputByReadGroup,
final Map<String, SAMFileHeader> headerMap,
final SAMFileHeader singleOutHeader,
final int maxRecordsInRam) {
this.outputByReadGroup = outputByReadGroup;
if (outputByReadGroup) {
for (final Map.Entry<String, SAMFileHeader> entry : headerMap.entrySet()) {
final String readGroupId = entry.getKey();
final SAMFileHeader outHeader = entry.getValue();
final SortingCollection<SAMRecord> sorter = SortingCollection.newInstance(SAMRecord.class, new BAMRecordCodec(outHeader), new SAMRecordQueryNameComparator(), maxRecordsInRam);
sorterMap.put(readGroupId, sorter);
}
singleSorter = null;
} else {
singleSorter = SortingCollection.newInstance(SAMRecord.class, new BAMRecordCodec(singleOutHeader), new SAMRecordQueryNameComparator(), maxRecordsInRam);
}
}
示例2: sortInputs
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
/**
* Merge the inputs and sort them by adding each input's content to a single SortingCollection.
* <p/>
* NB: It would be better to have a merging iterator as in MergeSamFiles, as this would perform better for pre-sorted inputs.
* Here, we are assuming inputs are unsorted, and so adding their VariantContexts iteratively is fine for now.
* MergeVcfs exists for simple merging of presorted inputs.
*
* @param readers - a list of VCFFileReaders, one for each input VCF
* @param outputHeader - The merged header whose information we intend to use in the final output file
*/
private SortingCollection<VariantContext> sortInputs(final List<VCFFileReader> readers, final VCFHeader outputHeader) {
final ProgressLogger readProgress = new ProgressLogger(log, 25000, "read", "records");
// NB: The default MAX_RECORDS_IN_RAM may not be appropriate here. VariantContexts are smaller than SamRecords
// We would have to play around empirically to find an appropriate value. We are not performing this optimization at this time.
final SortingCollection<VariantContext> sorter =
SortingCollection.newInstance(
VariantContext.class,
new VCFRecordCodec(outputHeader, VALIDATION_STRINGENCY != ValidationStringency.STRICT),
outputHeader.getVCFRecordComparator(),
MAX_RECORDS_IN_RAM,
TMP_DIR);
int readerCount = 1;
for (final VCFFileReader reader : readers) {
log.info("Reading entries from input file " + readerCount);
for (final VariantContext variantContext : reader) {
sorter.add(variantContext);
readProgress.record(variantContext.getContig(), variantContext.getStart());
}
reader.close();
readerCount++;
}
return sorter;
}
示例3: run
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
/**
* @param maxMemory - in megabytes
* @throws IOException
*
*/
public void run(int maxMemory) throws IOException {
try (
PrintWriter writer = NgbFileUtils.isGzCompressed(outputFile.getName()) ?
new PrintWriter(new OutputStreamWriter(new BlockCompressedOutputStream(outputFile), UTF_8)) :
new PrintWriter(outputFile, UTF_8);
AsciiLineReader reader = NgbFileUtils.isGzCompressed(outputFile.getName()) ?
new AsciiLineReader(new BlockCompressedInputStream(inputFile)) :
new AsciiLineReader(new FileInputStream(inputFile))
) {
SortableRecordCodec codec = new SortableRecordCodec();
SortingCollection cltn = SortingCollection.newInstance(
SortableRecord.class, codec, comparator, maxMemory * 1024 * 1024 / ESTIMATED_RECORD_SIZE, tmpDir);
Parser parser = getParser();
String firstDataRow = writeHeader(reader, writer);
if (firstDataRow != null && !firstDataRow.isEmpty()) {
cltn.add(parser.createRecord(firstDataRow));
}
SortableRecord next;
while ((next = parser.readNextRecord(reader)) != null) {
cltn.add(next);
}
CloseableIterator<SortableRecord> iter = cltn.iterator();
while (iter.hasNext()) {
SortableRecord al = iter.next();
writer.println(al.getText());
}
iter.close();
}
}
示例4: run
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
/**
* @param maxMemory - in megabytes
* @throws IOException
*
*/
public void run(int maxMemory) throws IOException {
try (
PrintWriter writer = NgbFileUtils.isGzCompressed(outputFile.getName()) ?
new PrintWriter(new OutputStreamWriter(new BlockCompressedOutputStream(outputFile), UTF_8)) :
new PrintWriter(outputFile, UTF_8);
AsciiLineReader reader = NgbFileUtils.isGzCompressed(inputFile.getName()) ?
new AsciiLineReader(new BlockCompressedInputStream(inputFile)) :
new AsciiLineReader(new FileInputStream(inputFile))
) {
SortableRecordCodec codec = new SortableRecordCodec();
SortingCollection cltn = SortingCollection.newInstance(
SortableRecord.class, codec, comparator, maxMemory * 1024 * 1024 / ESTIMATED_RECORD_SIZE, tmpDir);
Parser parser = getParser();
String firstDataRow = writeHeader(reader, writer);
if (firstDataRow != null && !firstDataRow.isEmpty()) {
cltn.add(parser.createRecord(firstDataRow));
}
SortableRecord next;
while ((next = parser.readNextRecord(reader)) != null) {
cltn.add(next);
}
CloseableIterator<SortableRecord> iter = cltn.iterator();
while (iter.hasNext()) {
SortableRecord al = iter.next();
writer.println(al.getText());
}
iter.close();
}
}
示例5: newSortingCollection
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
private synchronized SortingCollection<CLUSTER_OUTPUT_RECORD> newSortingCollection() {
final int maxRecordsInRam =
Math.max(1, maxReadsInRamPerTile /
barcodeRecordWriterMap.size());
return SortingCollection.newInstance(
outputRecordClass,
codecPrototype.clone(),
outputRecordComparator,
maxRecordsInRam,
tmpDirs);
}
示例6: makeSortingCollection
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
private SortingCollection<String> makeSortingCollection() {
final String name = getClass().getSimpleName();
final File tmpDir = IOUtil.createTempDir(name, null);
tmpDir.deleteOnExit();
// 256 byte for one name, and 1/10 part of all memory for this, rough estimate
long maxNamesInRam = Runtime.getRuntime().maxMemory() / 256 / 10;
return SortingCollection.newInstance(
String.class,
new StringCodec(),
String::compareTo,
(int) Math.min(maxNamesInRam, Integer.MAX_VALUE),
tmpDir
);
}
示例7: 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8: writeHeader
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
@Override
public void writeHeader(VCFHeader header) {
this.delegate.writeHeader(header);
this.sorter =
SortingCollection.newInstance(
VariantContext.class,
new VCFRecordCodec(header),
header.getVCFRecordComparator(),
VcfIndexTabix.this.writingSortingCollection.getMaxRecordsInRam(),
VcfIndexTabix.this.writingSortingCollection.getTmpPaths()
);
}
示例9: newInstance
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
public static SortingCollection<VcfLine> newInstance(int maxRecords, String tempDir) {
return SortingCollection.newInstance(VcfLine.class, new VcfLineCodec(), new VcfLineComparator(), maxRecords,
new File(tempDir));
}
示例10: run
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
public void run() throws IOException {
FileInputStream fis = null;
PrintWriter writer = null;
try {
fis = new FileInputStream(inputFile);
Writer rawWriter;
if (writeStdOut) {
rawWriter = new OutputStreamWriter(System.out);
} else {
rawWriter = new FileWriter(this.outputFile);
}
writer = new PrintWriter(new BufferedWriter(rawWriter));
SortableRecordCodec codec = new SortableRecordCodec();
SortingCollection cltn = SortingCollection.newInstance(SortableRecord.class, codec, comparator, maxRecords, tmpDir);
Parser parser = getParser();
AsciiLineReader reader = new AsciiLineReader(fis);
String firstDataRow = writeHeader(reader, writer);
if (firstDataRow != null) {
cltn.add(parser.createRecord(firstDataRow));
}
SortableRecord next = null;
while ((next = parser.readNextRecord(reader)) != null) {
cltn.add(next);
}
CloseableIterator<SortableRecord> iter = cltn.iterator();
while (iter.hasNext()) {
SortableRecord al = iter.next();
writer.println(al.getText());
}
iter.close();
} finally {
if (fis != null) fis.close();
if (writer != null) writer.close();
}
}
示例11: add
import htsjdk.samtools.util.SortingCollection; //导入方法依赖的package包/类
@Override
public void add(final VariantContext ctx) {
if(prev_contig==null || !ctx.getContig().equals(prev_contig)) {
dump();
prev_contig=ctx.getContig();
}
if(ctx.isFiltered() && !this.acceptFiltered)
{
//add to delegate without registering the SPLIT name
super.add(ctx);
return;
}
final Set<String> splitNames = getSplitNamesFor(ctx);
if(splitNames.isEmpty())
{
super.add(ctx);
return;
}
if(this.sortingcollection==null) {
/* create sorting collection for new contig */
this.sortingcollection = SortingCollection.newInstance(
Interval.class,
new IntervalCodec(),
new IntervalComparator(),
this.maxRecordsInRam,
this.tmpDir.toPath()
);
this.sortingcollection.setDestructiveIteration(true);
}
for(final String spltiName:splitNames)
{
this.sortingcollection.add(
new Interval(ctx.getContig(), ctx.getStart(), ctx.getEnd(),false,spltiName));
}
super.add(new VariantContextBuilder(ctx).attribute(
this.splitInfoKey,
new ArrayList<>(splitNames)).
make());
}
示例12: 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13: 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14: 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();
}
}