Java SAMRecordIterator.close方法代码示例

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
private static File queryNameSortedBAM(final SamReader reader, final QueryInterval[] intervals, final String name) throws IOException {

        final SAMFileHeader header = reader.getFileHeader().clone();
        header.setSortOrder(SAMFileHeader.SortOrder.queryname);

        final File file = File.createTempFile(name, ".bam");
        final SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(header, false, file);

        final SAMRecordIterator iterator = reader.queryOverlapping(intervals);
        while (iterator.hasNext()) {
            writer.addAlignment(iterator.next());
        }

        iterator.close();
        writer.close();

        return file;
    }
 

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
/**
 * Given a SamReader, find all reads within a region (ref:start-end) that span a splice junction and tally the number of times
 * each junction is spanned. Optionally tally the average values of "tallyTagName" tags (eg. NM).
 * 
 * @param reader
 * @param ref
 * @param start
 * @param end
 * @param orient
 * @param minOverlap
 * @param tallyTagName
 * @param separateReadCounts
 * @return
 */
public static SortedMap<GenomeSpan, MappedReadCounter> countJunctions(SamReader reader, String ref, int start, int end, Orientation orient, int minOverlap, String tallyTagName) {
    SAMRecordIterator it = reader.query(ref, start, end, true);
    SortedMap<GenomeSpan, MappedReadCounter> counters = new TreeMap<GenomeSpan, MappedReadCounter>();
    
    while (it.hasNext()) {
        SAMRecord read = it.next();
        if (read.isSecondaryOrSupplementary() || read.getDuplicateReadFlag() || read.getNotPrimaryAlignmentFlag() || read.getReadUnmappedFlag() || read.getSupplementaryAlignmentFlag()) {
            // skip all secondary / duplicate / unmapped reads
            continue;
        }
       
        if (isJunctionSpanning(read)) {
            for (GenomeSpan junction: getJunctionsForRead(read, orient, minOverlap)) {
                if (!counters.containsKey(junction)) {
                    counters.put(junction, new MappedReadCounter(tallyTagName));
                }
                
                counters.get(junction).addRead(read);
            }
        }
    }
    it.close();
    return counters;
}
 

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
private void scan(final SamReader in) 
{
final SAMSequenceDictionary dict=in.getFileHeader().getSequenceDictionary();
if(dict==null) throw new RuntimeException("Sequence dictionary missing...");
final SAMRecordIterator iter=in.iterator();
final SAMSequenceDictionaryProgress progress=new SAMSequenceDictionaryProgress(dict);		
while(iter.hasNext() && !this.out.checkError())
	{
	final  SAMRecord rec=progress.watch(iter.next());
	if(rec.getReadUnmappedFlag()) continue;
	for(final PslAlign a:makePslAlign(rec,dict))
		{
		out.println(toString(a,rec));
		}
	}
progress.finish();
iter.close();
}
 

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
private void scan(final SamReader in) throws IOException
 	{
 	SAMRecordIterator iter=in.iterator();
 	while(iter.hasNext())
{
 		final SAMRecord rec = iter.next();
 		String sampleName= this.partition.getPartion(rec);
 		if(sampleName==null || sampleName.isEmpty()) sampleName="__UNDEFINED_"+this.partition.name().toUpperCase()+"_";
 		
 		Counter<Integer> counter = this.lengths.get(sampleName);
 		if(counter==null) {
 			counter = new Counter<>();
 			 this.lengths.put(sampleName,counter);
 		}
 		final int len = rec.getReadLength();
 		counter.incr(len);
 		this.max_length=Math.max(max_length, len);
 		
}
 	iter.close();
 	}
 

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
private static void writeToSlice(final String path, final SamReader reader, final QueryInterval[] intervals) {
    final File outputBAM = new File(path);
    final SAMFileWriter writer = new SAMFileWriterFactory().makeBAMWriter(reader.getFileHeader(), true, outputBAM);
    final SAMRecordIterator iterator = reader.queryOverlapping(intervals);
    while (iterator.hasNext()) {
        writer.addAlignment(iterator.next());
    }
    iterator.close();
    writer.close();
}
 

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
@NotNull
public List<VariantContext> mergeVariants(@NotNull final PotentialMNVRegion potentialMnvRegion) {
    if (potentialMnvRegion.potentialMnvs().size() == 0) {
        return potentialMnvRegion.variants();
    } else {
        final SAMRecordIterator samIterator = queryBam(potentialMnvRegion);
        final MNVRegionValidator regionValidator = validateMNVs(samIterator, potentialMnvRegion);
        samIterator.close();
        return outputVariants(regionValidator);
    }
}
 

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
public static int getSamReadLength(SamReader reader, int recordsToScan) {
	int i = 0;
	int size = 0;
    SAMRecordIterator it = reader.iterator();
    while (it.hasNext() && i < recordsToScan) {
    	SAMRecord read = it.next();
    	size = Math.max(size,  read.getReadLength());
    	i++;
    }
    it.close();
    return size;
}
 

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
/** 
 * Find reads that overlap a given genomic region
 * @param reader
 * @param pos
 * @param orient
 * @param readLength
 * @param minOverlap
 * @param allowGaps
 * @return
 */
public static List<SAMRecord> findOverlappingReads(SamReader reader, GenomeSpan pos, Orientation orient, int readLength, int minOverlap, boolean allowGaps) {
	List<SAMRecord> out = new ArrayList<SAMRecord>();

	SAMRecordIterator it = reader.query(pos.ref, pos.start - readLength + minOverlap, pos.start + readLength - minOverlap, true);
    while (it.hasNext()) {
        SAMRecord read = it.next();
        if (read.isSecondaryOrSupplementary() || read.getDuplicateReadFlag() || read.getNotPrimaryAlignmentFlag() || read.getReadUnmappedFlag() || read.getSupplementaryAlignmentFlag()) {
            // skip all secondary / duplicate / unmapped reads
            continue;
        }
        
        if (!allowGaps) {
            // skip all reads with gaps
            for (CigarElement el: read.getCigar().getCigarElements()) {
                if (el.getOperator() == CigarOperator.N) {
                    continue;
                }
            }
        }
        
        if (ReadUtils.getFragmentEffectiveStrand(read, orient) != pos.strand) {
        	continue;
        }
        
        for (GenomeSpan region: ReadUtils.getJunctionFlankingRegions(read, orient, minOverlap)) {
        	if (region.start <= (pos.start - minOverlap) && region.end >= (pos.start + minOverlap)) {
        		out.add(read);
        		break;
        	}
        }
    }
    it.close();
	return out;
}
 

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
/**
 * Helper function that writes reads from iterator it into writer out, updating each SAMRecord along the way
 * according to the newOrder mapping from dictionary index -> index.  Name is used for printing only.
 */
private void writeReads(final SAMFileWriter out,
                        final SAMRecordIterator it,
                        final Map<Integer, Integer> newOrder,
                        final String name) {
    long counter = 0;
    log.info("  Processing " + name);

    while (it.hasNext()) {
        counter++;
        final SAMRecord read = it.next();
        final int oldRefIndex = read.getReferenceIndex();
        final int oldMateIndex = read.getMateReferenceIndex();
        final int newRefIndex = newOrderIndex(read, oldRefIndex, newOrder);

        read.setHeader(out.getFileHeader());
        read.setReferenceIndex(newRefIndex);

        final int newMateIndex = newOrderIndex(read, oldMateIndex, newOrder);
        if (oldMateIndex != -1 && newMateIndex == -1) { // becoming unmapped
            read.setMateAlignmentStart(0);
            read.setMateUnmappedFlag(true);
            read.setAttribute(SAMTag.MC.name(), null);      // Set the Mate Cigar String to null
        }
        read.setMateReferenceIndex(newMateIndex);

        out.addAlignment(read);
    }

    it.close();
    log.info("Wrote " + counter + " reads");
}
 

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
public static HeaderInfo getHeaderFromBAMFile(Storage.Objects storage, String BAMPath, Iterable<Contig> explicitlyRequestedContigs) throws IOException {
  HeaderInfo result = null;

  // Open and read start of BAM
  LOG.info("Reading header from " + BAMPath);
  final SamReader samReader = BAMIO
      .openBAM(storage, BAMPath, ValidationStringency.DEFAULT_STRINGENCY);
  final SAMFileHeader header = samReader.getFileHeader();
  Contig firstContig = getFirstExplicitContigOrNull(header, explicitlyRequestedContigs);
  if (firstContig == null) {
    final SAMSequenceRecord seqRecord = header.getSequence(0);
    firstContig = new Contig(seqRecord.getSequenceName(), -1, -1);
  }

  LOG.info("Reading first chunk of reads from " + BAMPath);
  final SAMRecordIterator recordIterator = samReader.query(
      firstContig.referenceName, (int)firstContig.start + 1, (int)firstContig.end + 1, false);

  Contig firstShard = null;
  while (recordIterator.hasNext() && result == null) {
    SAMRecord record = recordIterator.next();
    final int alignmentStart = record.getAlignmentStart();
    if (firstShard == null && alignmentStart > firstContig.start &&
        (alignmentStart < firstContig.end || firstContig.end == -1)) {
      firstShard = new Contig(firstContig.referenceName, alignmentStart, alignmentStart);
      LOG.info("Determined first shard to be " + firstShard);
      result = new HeaderInfo(header, firstShard);
    }
  }
  recordIterator.close();
  samReader.close();

  if (result == null) {
    throw new IOException("Did not find reads for the first contig " + firstContig.toString());
  }
  LOG.info("Finished header reading from " + BAMPath);
  return result;
}
 

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
private int call(final String inputName) throws Exception {
PrintWriter out=null;
SamReader sfr=null;
final SamJsonWriterFactory factory =SamJsonWriterFactory.newInstance().
		printHeader(this.print_header).
		printReadName(!this.disable_readName).
		printAttributes(!this.disable_atts).
		expandFlag(this.expflag).
		expandCigar(this.excigar)
		;
SAMFileWriter swf=null;
try
	{
	sfr = super.openSamReader(inputName);
	out = super.openFileOrStdoutAsPrintWriter(this.output);
	swf = factory.open(sfr.getFileHeader(), out);
	final SAMRecordIterator iter=sfr.iterator();
	while(iter.hasNext() && !out.checkError())
		{
		swf.addAlignment(iter.next());
		}
	iter.close();
	out.flush();
	swf.close();swf=null;
	LOG.info("done");
	return 0;
	}
catch(final Exception err) {
	LOG.error(err);
	return -1;
	}
finally 	{
	CloserUtil.close(sfr);
	CloserUtil.close(swf);
	}
}
 

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
/** return DP at given position */
private int fetchDP(final VariantContext ctx,final String sample,List<SamReader> samReaders)
	{
	int depth=0;
	if(samReaders==null) samReaders=Collections.emptyList();
	for(final SamReader sr: samReaders)
		{
		final SAMRecordIterator iter=sr.query(ctx.getContig(), ctx.getStart(), ctx.getEnd(), false);
		while(iter.hasNext())
			{
			final SAMRecord rec=iter.next();
			if(rec.getReadUnmappedFlag()) continue;
			if(filter.filterOut(rec)) continue;
			final SAMReadGroupRecord rg=rec.getReadGroup();
			if(!sample.equals(rg.getSample())) continue;
			final Cigar cigar=rec.getCigar();
			if(cigar==null) continue;
			int refPos=rec.getAlignmentStart();
			for(final CigarElement ce:cigar.getCigarElements())
				{
				if( refPos > ctx.getEnd() ) break;
				if(!ce.getOperator().consumesReferenceBases()) continue;
				if( ce.getOperator().consumesReadBases())
					{
					for(int n=0;n< ce.getLength();++n )
						{
						if( refPos+n < ctx.getStart() ) continue;
						if( refPos+n > ctx.getEnd()) break;
						depth++;
						}
					}
				refPos+= ce.getLength();
				}
			}
		iter.close();
		}
depth /= ( 1 + ctx.getEnd() - ctx.getStart() );
return depth;
}
 

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
private void scan(final SamReader r) {
final SAMRecordIterator iter=r.query(
			interval.getContig(),
			interval.getStart(),
			interval.getEnd(),
			false
			);
while(iter.hasNext())
	{
	final SAMRecord rec=iter.next();
	if(rec.getReadUnmappedFlag()) continue;
	if(this.samRecordFilter.filterOut(rec)) continue;

	if(!this.interval.getContig().equals(rec.getReferenceName())) continue;
	if(super.readRight.apply(rec) < this.interval.getStart()) 
		{
		continue;
		}
	if(super.readLeft.apply(rec) > this.interval.getEnd()) {
		break;
		}
	
	final String group=this.groupBy.apply(rec.getReadGroup());
	if(group==null) continue;
	PartitionImage partition =  this.key2partition.get(group);
	if( partition == null)
		{
		partition=new PartitionImage(group);
		this.key2partition.put(group,partition);
		}
	partition.add(rec);
	}
iter.close();
}
 

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
private void scan(SamReader in) 
{
SAMSequenceDictionary dict=in.getFileHeader().getSequenceDictionary();
if(dict==null) throw new RuntimeException("Sequence dictionary missing");
SAMRecordIterator iter=in.iterator();
SAMSequenceDictionaryProgress progress=new SAMSequenceDictionaryProgress(dict);

while(iter.hasNext())
	{
	final SAMRecord rec=iter.next();
	if(rec.getReadUnmappedFlag()) continue;
	if(rec.isSecondaryOrSupplementary()) continue;
	progress.watch(rec);
	
	if(isWeird(rec,dict))
		{
		this.weird.addAlignment(rec);
		continue;
		}
	
	for(CigarElement ce:rec.getCigar().getCigarElements())
		{
		if(ce.getOperator().equals(CigarOperator.N))
			{
			scanRead(rec,dict);
			break;
			}
		}	
	}
iter.close();
progress.finish();
}
 

import htsjdk.samtools.SAMRecordIterator; //导入方法依赖的package包/类
private void scanFile(SamReader r) {
final SAMSequenceDictionaryProgress progess= new SAMSequenceDictionaryProgress(r.getFileHeader());
final SAMRecordIterator iter = r.iterator();
while(iter.hasNext())
	{
	analyseSamRecord(progess.watch(iter.next()));
	}
progess.finish();
iter.close();
}