Examples of SAMRecord

Examples of net.sf.samtools.SAMRecord

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  }
 
  @Test (groups = "unit")
  public void testHardClipping() {
    List<SAMRecord> reads = new ArrayList<SAMRecord>();
    SAMRecord read1 = newRecord(6169757, "217M75S", 292);
    SAMRecord read2 = newRecord(6170072, "215H77M", 77);
//    reads.add(newRecord(6169757, "217M75S", 292));
//    reads.add(newRecord(6170072, "215H77M", 77));
   
    reads.add(read1);
    reads.add(read2);
   
    List<SAMRecord> outputList = cc.processRead(reads);
    assertEquals(outputList.size(), 1);
    SAMRecord combined = outputList.get(0);
    assertEquals(combined.getAlignmentStart(), 6169757);
    assertEquals(combined.getCigarString(), "215M100D77M");
    assertEquals(read1.getReadLength(), 292);
    assertEquals(read2.getReadLength(), 292);
  }
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Examples of net.sf.samtools.SAMRecord

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    assertEquals(read1.getReadLength(), 292);
    assertEquals(read2.getReadLength(), 292);
  }
 
  private SAMRecord newRecord(int pos, String cigar, int length) {
    SAMRecord record = new SAMRecord(null);
    record.setReferenceName("chr21");
    record.setAlignmentStart(pos);
    record.setCigarString(cigar);
    record.setReadNegativeStrandFlag(false);
    char[] bases = new char[length];
    Arrays.fill(bases, 'A');
    record.setReadString(String.valueOf(bases));
    return record;
  }
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