Package net.sf.samtools

Examples of net.sf.samtools.SAMRecord

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    c2r.init(ref);
   
    IndelShifter indelShifter = new IndelShifter();

    for (SAMRecord read : reader) {
      SAMRecord shiftedRead = indelShifter.shiftIndelsLeft(read, c2r);
      writer.addAlignment(shiftedRead);
    }
   
    writer.close();
    reader.close();
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*/
   
//    String readStr = "chr11_118380033_118380233_2__numedges:341_totaledgecounts:133107_medianedgecount:417_minedgecount:4_terminatedatrepeat:false  0  chr11  118379934  239  235M3I164M  *  0  0  GGTTAGAATCAGAGAATATCAATGCTAAAAGGATTATGAGAATCACCCACTTTACCTACTTATTTTCTACATTTAAAAAAAAAAATCTAAGCTCCAAAGAAGTTAAGTGATTTGGCCCACATTGGACTGAAACTTGGCGCACCTGTCTCTCGGTGCAGTGTTCTTCCAGTACATATTGTGTGATCACCTGTCAGCTAAGGACTCAAGACCATACCCATACTCTTCTGCTGTACTGGCTGTTTTACCAGCACTGAGGCTTAAATAGCTAGTAATAACCTGACTTCACTTTTTAGTTGTTACTAAAGAAAACTAAGAACCATTTTTATTAGATAGTCAGATTTTGGTTACAATACCAGATACATCTCCATGGCATTTTCCATCAGTTCTAATGAATTTGATTAG  *  XE:i:9  XF:i:0  XN:i:0  AS:i:388";
    String readStr = "chr11_118380033_118380233_2__numedges:341_totaledgecounts:133107_medianedgecount:417_minedgecount:4_terminatedatrepeat:false  0  chr11  110000001  239  100M800D135M3I164M  *  0  0  GGTTAGAATCAGAGAATATCAATGCTAAAAGGATTATGAGAATCACCCACTTTACCTACTTATTTTCTACATTTAAAAAAAAAAATCTAAGCTCCAAAGAAGTTAAGTGATTTGGCCCACATTGGACTGAAACTTGGCGCACCTGTCTCTCGGTGCAGTGTTCTTCCAGTACATATTGTGTGATCACCTGTCAGCTAAGGACTCAAGACCATACCCATACTCTTCTGCTGTACTGGCTGTTTTACCAGCACTGAGGCTTAAATAGCTAGTAATAACCTGACTTCACTTTTTAGTTGTTACTAAAGAAAACTAAGAACCATTTTTATTAGATAGTCAGATTTTGGTTACAATACCAGATACATCTCCATGGCATTTTCCATCAGTTCTAATGAATTTGATTAG  *  XE:i:9  XF:i:0  XN:i:0  AS:i:388";
    SamStringReader rdr = new SamStringReader(new SAMFileHeader());
    SAMRecord read = rdr.getRead(readStr);
    System.out.println("read: " + read);
    System.out.println(read.getSAMString());
    System.out.println(read.getAlignmentStart());
    System.out.println(read.getAlignmentEnd());
    System.out.println(read.getReadLength());
  }
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    reads.add(newRecord(6162064, "129S120M", 249));
    reads.add(newRecord(6161985, "79M170S", 249));
   
    List<SAMRecord> outputList = cc.processRead(reads);
    assertEquals(outputList.size(), 1);
    SAMRecord combined = outputList.get(0);
    assertEquals(combined.getAlignmentStart(), 6161985);
    assertEquals(combined.getCigarString(), "79M50I120M");
  }
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    reads.add(newRecord(6161985, "129M120S", 249));
    reads.add(newRecord(6162064, "129S120M", 249));
   
    List<SAMRecord> outputList = cc.processRead(reads);
    assertEquals(outputList.size(), 1);
    SAMRecord combined = outputList.get(0);
    assertEquals(combined.getAlignmentStart(), 6161985);
    assertEquals(combined.getCigarString(), "79M50I120M");
  }
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    reads.add(newRecord(16085602, "60S65M", 125));
    reads.add(newRecord(16085517, "60M65S", 125));
   
    List<SAMRecord> outputList = cc.processRead(reads);
    assertEquals(outputList.size(), 1);
    SAMRecord combined = outputList.get(0);
    assertEquals(combined.getAlignmentStart(), 16085517);
    assertEquals(combined.getCigarString(), "60M25D65M");
    assertEquals(combined.getReadLength(), 125);
  }
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    reads.add(newRecord(16085605, "49S62M", 111));
    reads.add(newRecord(16085517, "53M58S", 111));
   
    List<SAMRecord> outputList = cc.processRead(reads);
    assertEquals(outputList.size(), 1);
    SAMRecord combined = outputList.get(0);
    assertEquals(combined.getAlignmentStart(), 16085517);
    assertEquals(combined.getCigarString(), "49M39D62M");
    assertEquals(combined.getReadLength(), 111);
  }
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    reads.add(newRecord(16085717, "300S200M", 500));
    reads.add(newRecord(33141553, "199S102M199S", 500));
   
    List<SAMRecord> outputList = cc.processRead(reads);
    assertEquals(outputList.size(), 1);
    SAMRecord combined = outputList.get(0);
    assertEquals(combined.getAlignmentStart(), 16085517);
    assertEquals(combined.getCigarString(), "200M100I200M");
  }
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    reads.add(newRecord(30826191, "90S51M43S", 184));
    reads.add(newRecord(30726192, "141S43M", 184));
   
    List<SAMRecord> outputList = cc.processRead(reads);
    assertEquals(outputList.size(), 1);
    SAMRecord combined = outputList.get(0);
    assertEquals(combined.getAlignmentStart(), 30726101);
    assertEquals(combined.getCigarString(), "90M50I44M");
  }
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    reads.add(newRecord(11032656, "63M31S", 94));
    reads.add(newRecord(214990735, "34S60M", 94));
   
    List<SAMRecord> outputList = cc.processRead(reads);
    assertEquals(outputList.size(), 2);
    SAMRecord read1 = outputList.get(0);
    SAMRecord read2 = outputList.get(1);
    assertEquals(read1.getAlignmentStart(), 11032656);
    assertEquals(read2.getAlignmentStart(), 214990735);
  }
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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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Related Classes of net.sf.samtools.SAMRecord

  • abra.bamsplitter.BamSplitter
  • abra.bamsplitter.BamSplitterThread
  • abra.BetaPairValidatingRealignmentWriter
  • abra.cadabra.ForwardShiftInsertIterator
  • abra.cadabra.ReadLocusReader$ReadLocusIterator
  • abra.cadabra.SomaticLocusCaller
  • abra.CombineChimera3
  • abra.CombineChimeraTest
  • abra.ContigChopper
  • abra.IndelShifter
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