Java SAMFileReader.setValidationStringency方法代码示例

import net.sf.samtools.SAMFileReader; //导入方法依赖的package包/类
/**
 * Get the reads from the appropriate source (implementation-specific).
 * Loads data to the fivePrimesList and hitsCountList
 */
public void sourceReads() {
	this.initialize();
	SAMFileReader reader = new SAMFileReader(file);
	reader.setValidationStringency(ValidationStringency.SILENT);
	CloseableIterator<SAMRecord> iter = reader.iterator();
	Collection<SAMRecord> byRead = new ArrayList<SAMRecord>();
	String lastread = null;
	while (iter.hasNext()) {
	    SAMRecord record = iter.next();
	    
	    if (record.getReadUnmappedFlag()) {continue; }
	    if (lastread == null || !lastread.equals(record.getReadName())) {
	    	processRead(byRead);
	    	byRead.clear();
	    }
	    lastread = record.getReadName();
	    byRead.add(record);
		    
	}
	processRead(byRead);
	iter.close();
	reader.close();
   }
 

import net.sf.samtools.SAMFileReader; //导入方法依赖的package包/类
public SAMStats(boolean bowtie1, boolean bowtie2){
this.bowtie1 = bowtie1;
this.bowtie2 = bowtie2;
histo = new RealValuedHistogram(0, 1000, 100);
SAMFileReader reader = new SAMFileReader(System.in);
reader.setValidationStringency(ValidationStringency.SILENT);
      CloseableIterator<SAMRecord> iter = reader.iterator();
      while (iter.hasNext()) {
          SAMRecord record = iter.next();
          if(readLen==-1)
          	readLen = record.getReadLength();
          if(bowtie1)
          	processBT1SAMRecord(record);
          else if(bowtie2)
          	processBT2SAMRecord(record);
          else
          	processSAMRecord(record);
      }
      iter.close();
      reader.close();        
  }
 

import net.sf.samtools.SAMFileReader; //导入方法依赖的package包/类
public BamRegionsMap(File bamfile, GenomeInfo ginfo, String validate, int minmapqual) throws IOException {

        this.ginfo = ginfo;
        this.minmapqual = minmapqual;
        if (bamfile != null) {
            bamreader = new SAMFileReader(bamfile);
            if (validate.equals("STRICT")) {
                bamreader.setValidationStringency(SAMFileReader.ValidationStringency.STRICT);
            } else if (validate.equals("LENIENT")) {
                bamreader.setValidationStringency(SAMFileReader.ValidationStringency.LENIENT);
            } else {
                bamreader.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);
            }

            bamiterator = bamreader.iterator();
            if (bamiterator.hasNext()) {
                record = bamiterator.next();
                curchr = record.getReferenceName();
            }

        } else {
            bamreader = null;
            bamiterator = null;
        }

        regions = new HashMap<Integer, ArrayList<SAMRecord>>(128);
    }
 

import net.sf.samtools.SAMFileReader; //导入方法依赖的package包/类
@Override
public void run() {

    theslog.log(true, "Pass one: " + bamfile.getAbsolutePath());

    // set up input/output objects using SAM library
    SAMFileReader inputSam = new SAMFileReader(bamfile);
    inputSam.setValidationStringency(SAMFileReader.ValidationStringency.SILENT);

    for (final SAMRecord record : inputSam) {

        if (record.getReadUnmappedFlag()) {
            // if read is unaligned, output coordinates into a bed file
            processOneUnalignedRecord(record);
        } else {
            // if aligned, then make thesaurus entries
            int mapqual = record.getMappingQuality();
            // only consider reads with a minimum mapping quality
            // (this here is not a "real" mapping quality, but a proxy for number of mismatches)
            if (mapqual >= minmapqual) {
                // check that read is aligned                
                processOneRecord(record);
            }
        }
    }

    // and close the input file stream
    inputSam.close();
}
 

import net.sf.samtools.SAMFileReader; //导入方法依赖的package包/类
/**
 * Reads the read alignments
 * reference ID format is
 *   [genome|nogenome]:[library]:[referenceID]
 * e.g.
 *   genome:miRNA:hsa-mir-486-1:MI0002470:Homo:sapiens:miR-486:stem-loop
 * 
 * @param path_readAlignments
 * @throws IOException 
 */

public boolean read_Reads(SAMFileReader inputSam) throws IOException{
	inputSam.setValidationStringency(ValidationStringency.SILENT);
	//inputSam.setValidationStringency(ValidationStringency.LENIENT);

	// TODO: put this if/else back when we're done testing
	//if(inputSam.getFileHeader().getSortOrder().equals(SAMFileHeader.SortOrder.queryname)){
	SAMRecord thisRecord;
	HashMap<SAMRecord, String> thisRead = new HashMap<SAMRecord, String>(); 
	SAMRecordIterator it = inputSam.iterator();
	String lastReadID = null;
	while(it.hasNext()){
		//count++;
		thisRecord = it.next();

		//System.out.println(thisRecord.getReferenceName());
		if(!thisRecord.getReadName().equals(lastReadID)  &&  lastReadID != null){
			// new, non first
			assignRead(thisRead);
			thisRead = new HashMap<SAMRecord, String>();
		}

		// put the SAM record into the map with the library type as the value
		//thisRead.put(thisRecord, thisRecord.getReferenceName().split(":")[1]);

		if(_forceLibrary != null)
			thisRead.put(thisRecord, _forceLibrary);
		else
			thisRead.put(thisRecord, thisRecord.getReferenceName().split(":")[0]);
		lastReadID = thisRecord.getReadName();

	}
	// assign the final read!
	if(thisRead.size() > 0)
		assignRead(thisRead);

	/*}else{
	Thunder.printLineErr("ERROR: Input SAM file must be sorted by readID");
	inputSam.close();
	return false;
	}*/

	inputSam.close();
	return true;
}
 

import net.sf.samtools.SAMFileReader; //导入方法依赖的package包/类
/**
 * Get the reads from the appropriate source (implementation-specific).
 * Loads data to the fivePrimesList and hitsCountList
 */
public void sourceReads() {
	this.initialize();
	SAMFileReader reader = new SAMFileReader(file);
	reader.setValidationStringency(ValidationStringency.SILENT);
	CloseableIterator<SAMRecord> iter = reader.iterator();
	while (iter.hasNext()) {
	    SAMRecord record = iter.next();
	    
	    if (record.getReadUnmappedFlag()) {continue; }
	    float weight = 1/(float)record.getIntegerAttribute("NH");
	    
	    Read currRead = new Read();
        
	    List<AlignmentBlock> blocks = record.getAlignmentBlocks();
	    for(int a=0; a<blocks.size(); a++){ //Iterate over alignment blocks
	    	AlignmentBlock currBlock = blocks.get(a);
	    	int aStart = currBlock.getReferenceStart();
	    	int aEnd = aStart + currBlock.getLength()-1;
	    	int aLen = currBlock.getLength();
	    	boolean nearbyBlocks=true;
	    	while(nearbyBlocks && a<blocks.size()-1){
	    		if(blocks.get(a+1).getReferenceStart() - currBlock.getReferenceStart() < record.getReadLength()){
	    			aEnd = blocks.get(a+1).getReferenceStart() + blocks.get(a+1).getLength()-1;
	    			aLen += blocks.get(a+1).getLength();
	    			a++;
	    		}else{
	    			nearbyBlocks=false;
	    		}
	    	}
	    	
	    	ReadHit currHit = new ReadHit(
	    			record.getReferenceName().replaceFirst("^chr", ""),
	    			aStart, aEnd,
	    			record.getReadNegativeStrandFlag() ? '-' : '+',
	    			weight);
	   
	    	currRead.addHit(currHit);
		}	
	    addHits(currRead);
	}
	iter.close();
	reader.close();
   }
 

import net.sf.samtools.SAMFileReader; //导入方法依赖的package包/类
protected void countReads() {
readLength=-1;
totalHits=0;
totalWeight=0;

SAMFileReader reader = new SAMFileReader(inFile);
reader.setValidationStringency(ValidationStringency.SILENT);
CloseableIterator<SAMRecord> iter = reader.iterator();
while (iter.hasNext()) {
    currID++;
    SAMRecord record = iter.next();
    
    if (record.getReadUnmappedFlag()) {continue; }
    float weight = 1/(float)record.getIntegerAttribute("NH");
    if(readLength ==-1)
    	readLength = record.getReadLength();
    
    Read currRead = new Read((int)totalWeight);
       
    List<AlignmentBlock> blocks = record.getAlignmentBlocks();
    for(int a=0; a<blocks.size(); a++){ //Iterate over alignment blocks
    	AlignmentBlock currBlock = blocks.get(a);
    	int aStart = currBlock.getReferenceStart();
    	int aEnd = aStart + currBlock.getLength()-1;
    	int aLen = currBlock.getLength();
    	boolean nearbyBlocks=true;
    	while(nearbyBlocks && a<blocks.size()-1){
    		if(blocks.get(a+1).getReferenceStart() - currBlock.getReferenceStart() < record.getReadLength()){
    			aEnd = blocks.get(a+1).getReferenceStart() + blocks.get(a+1).getLength()-1;
    			aLen += blocks.get(a+1).getLength();
    			a++;
    		}else{
    			nearbyBlocks=false;
    		}
    	}
    	
    	ReadHit currHit = new ReadHit(gen,
			  currID,
			  record.getReferenceName().replaceFirst("^chr", ""), 
			  aStart, aEnd, 
			  record.getReadNegativeStrandFlag() ? '-' : '+',
			  weight);
   
    	currRead.addHit(currHit);
    	currID++;
	}	
    addHits(currRead);
    totalWeight++;
}
iter.close();
reader.close();
populateArrays();
  }