Examples of net.sf.samtools.SAMFileReader.queryOverlapping()

net.sf.samtools.SAMFileReader.queryOverlapping()
Iterate over records that overlap the given interval. Only valid to call this if hasIndex() == true.
Only a single open iterator on a given SAMFileReader may be extant at any one time. If you want to start a second iteration, the first one must be closed first.
Note that indexed lookup is not perfectly efficient in terms of disk I/O. I.e. some SAMRecords may be read and then discarded because they do not match the interval of interest.
Note that an unmapped read will be returned by this call if it has a coordinate for the purpose of sorting that is in the query region. @param sequence Reference sequence of interest. @param start 1-based, inclusive start of interval of interest. Zero implies start of the reference sequence. @param end 1-based, inclusive end of interval of interest. Zero implies end of the reference sequence. @return Iterator over the SAMRecords overlapping the interval.

    SAMFileReader reader = new SAMFileReader(new File(inputSam));
    reader.setValidationStringency(ValidationStringency.SILENT);
    
    for (Feature region : regions) {
      int count = 0;
      SAMRecordIterator iter = reader.queryOverlapping(region.getSeqname(), (int) region.getStart(), (int) region.getEnd());
      while (iter.hasNext()) {
        iter.next();
        count += 1;
      }
      iter.close();

View Full Code Here

      long numReadsWithAmbiguousBases = 0;
      long numReadsIntersectLt20Ambiguous = 0;
      long minMapq = 1000;
      long totalMapq = 0;
      
      CloseableIterator<SAMRecord> iter = reader.queryOverlapping(region.getSeqname(), (int) region.getStart(), (int) region.getEnd());
      
      while (iter.hasNext()) {
        SAMRecord read = iter.next();
        
        if (read.getMappingQuality() >= 10) {

View Full Code Here

      SAMFileReader reader = new SAMFileReader(new File(input));
      reader.setValidationStringency(ValidationStringency.SILENT);


      int[] counts = new int[thresholds.length];
      System.err.println(region.getDescriptor());
      Iterator<SAMRecord> iter = reader.queryOverlapping(region.getSeqname(), (int) region.getStart(), (int) region.getEnd());
      while (iter.hasNext()) {
        SAMRecord read = iter.next();
        if (!read.getReadUnmappedFlag()) {
          for (int i=0; i<thresholds.length; i++) {
            if (read.getMappingQuality() <= thresholds[i]) {

View Full Code Here

          SAMFileReader reader = new SAMFileReader(new File(input));
          reader.setValidationStringency(ValidationStringency.SILENT);
          
          Iterator<SAMRecord> iter;
          if (region != null) {
            iter = reader.queryOverlapping(region.getSeqname(), (int) region.getStart(), (int) region.getEnd());
          } else {
            iter = reader.iterator();
          }
          
          int candidateReadCount = 0;

View Full Code Here

TOP

All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.