Examples of SAMRecordIterator

Examples of net.sf.samtools.SAMRecordIterator

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    scFactory.losslessQS = true;
    scFactory.preserveReadNames = true;
    SequenceBaseProvider provider = new ByteArraySequenceBaseProvider(refBytes);

    SAMFileReader reader = new SAMFileReader(bamFile);
    SAMRecordIterator iterator = reader.query(seqName, 0, 0, false);
    List<CramRecord> records = new ArrayList<CramRecord>();

    PairedTemplateAssembler a = new PairedTemplateAssembler();
    int counter = 0;
    int bases = 0;
    long size = 0;
   
    Definition definition = new Definition();
    definition.contentId = "input.bam".getBytes();
    definition.formatMajor = 1;
    definition.formatMinor = 0;
    definition.magick = "CRAM".getBytes();
    Format format = new FormatFactory().createFormat(definition);

    SAMRecord samRecord = null;
    CramHeader cramHeader = createCramHeader(reader.getFileHeader());
    ByteArrayOutputStream hBaos= new ByteArrayOutputStream() ;
    Container hC = new Container() ;
    Block hBlock = new Block() ;
    hBlock.contentId=0;
    hBlock.contentType=0;
    hBlock.method = CompressionMethod.GZIP.byteValue() ;
    hC.blocks = new Block[]{hBlock} ;
    hC.containers= new Container[0] ;
    CramHeaderIO.write(cramHeader, hBaos) ;
    hBlock.data = hBaos.toByteArray() ;
    format.writeContainer(hC, hBaos) ;
    System.out.println("Header size: " + hBaos.size());
   
    for (int b = 0; b < maxRecords; b+=recordsPerBlock) {
      bases = 0 ;
      size = 0 ;
      for (int i = 0; i < recordsPerBlock; i++) {
        samRecord = iterator.next();
        a.addSAMRecord(samRecord);
        bases += samRecord.getReadLength();
      }

      for (int i = 0; i < recordsPerBlock; i++) {
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Examples of net.sf.samtools.SAMRecordIterator

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        String pathToBamFile = commandLine.getOptionValue("i");

        SAMFileReader reader = new SAMFileReader(new File(pathToBamFile));

        SAMRecordIterator iter = reader.iterator();

        long numBases = 0;
        long numGC = 0;


        while(iter.hasNext()){

            SAMRecord read = null;

            try {
                read = iter.next();
            } catch (RuntimeException e) {
                logger.warn( e.getMessage() );
            }

            if (read == null) {
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