Package net.sf.picard.util

Examples of net.sf.picard.util.IntervalList

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        String chr_id = "chr1";
        int start = 1;
        int end = 20;
//        int end = 247199724;
        Interval interval = new Interval(chr_id, start, end);
        IntervalList il = new IntervalList(samReader.getFileHeader());
        il.add(interval);
       
        SamLocusIterator sli = new SamLocusIterator(samReader, il, true);

        FileWriter fw = new FileWriter("/data/kimjh/WGS/simulation_test_chr1/seperate_10p/gatk/depth_diff.txt");
        BufferedWriter bw = new BufferedWriter(fw);
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        this.avgSeqQWindow = avgSeqQWindow;
    }

    public void setDeletionInfo(SAMFileReader samReader, ArrayList overlappedAreaList) {
        Interval interval = new Interval(getChr(), getWindowStart(), getWindowEnd());
        IntervalList il = new IntervalList(samReader.getFileHeader());
        il.add(interval);

        ArrayList locusList = new ArrayList();

        SamLocusIterator sli = new SamLocusIterator(samReader, il, true);
        for (Iterator<SamLocusIterator.LocusInfo> iter = sli.iterator(); iter.hasNext();) {
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Related Classes of net.sf.picard.util.IntervalList

  • solodel.bak
  • solodel.DeletionInfo
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