Examples of net.sf.samtools.SAMFileHeader

net.sf.samtools.SAMFileHeader

    }
  }
  
  public static void main(String[] args) {
    SAMFileReader reader = new SAMFileReader(new File("/home/lmose/dev/abra/1076/candidates.bam"));
    SAMFileHeader header = reader.getFileHeader();
    reader.close();
    header.setSortOrder(SortOrder.unsorted);
    
    SAMFileWriterFactory writerFactory = new SAMFileWriterFactory();
    writerFactory.setUseAsyncIo(false);
    SAMFileWriter writer = writerFactory.makeSAMOrBAMWriter(
        header, false, new File("/home/lmose/dev/abra/1076/test.bam"));

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  public static void main(String[] args) throws Exception {
    
//    String inputSam = "/home/lmose/dev/abra/region_tracker/normal.sort.bam";
    String inputSam = "/home/lmose/dev/abra/region_tracker/chr12.small.bam";
    SAMFileReader reader = new SAMFileReader(new File(inputSam));
    SAMFileHeader header = reader.getFileHeader();
    reader.close();
        
    CompareToReference2 c2r = null;
    
    SAMFileWriterFactory writerFactory = new SAMFileWriterFactory();
//    writerFactory.setUseAsyncIo(true);
    
    header.setSortOrder(SortOrder.unsorted);
    
    SAMFileWriter writer = writerFactory.makeSAMOrBAMWriter(
        header, false, new File("/home/lmose/dev/abra/region_tracker/out.bam"));
    
    Sam2Fastq s2f = new Sam2Fastq();

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    IndelShifter indelShifter = new IndelShifter();
    
    this.minIndelBuffer = minIndelBuffer;
    SamMultiMappingReader reader = new SamMultiMappingReader(input);
    
    SAMFileHeader header = reader.getFileHeader();
    header.setSortOrder(SortOrder.unsorted);
    
    SAMFileWriter outputReadsBam = new SAMFileWriterFactory().makeSAMOrBAMWriter(
        header, true, new File(output));


    for (List<SAMRecord> readList : reader) {

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  public void chopClopDrop(List<Feature> regions, String input, String output) {
    
    SAMFileReader reader = new SAMFileReader(new File(input));
    
    SAMFileHeader header = reader.getFileHeader();
    header.setSortOrder(SortOrder.unsorted);
    
    SAMFileWriter out = new SAMFileWriterFactory().makeSAMOrBAMWriter(
        header, true, new File(output));
    
    for (Feature region : regions) {

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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());

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    byteBuffer.get();
    return StringUtil.bytesToString(buf);
  }


  public static void main(String[] args) {
    SAMFileHeader h = new SAMFileHeader();
    SAMRecord r = new SAMRecord(h);
    r.setAttribute("OQ", "A:LKAS:LKASDJKL".getBytes());
    r.setAttribute("XA", 1333123);
    r.setAttribute("XB", (byte) 31);
    r.setAttribute("XB", 'Q');

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    for (RecordSource source : list) {
      mergeComment.append(" ").append(source.path);
    }


    resolveCollisions(list);
    SAMFileHeader header = mergeHeaders(list);
    header.addComment(mergeComment.toString());


    SAMFileWriter writer = null;
    if (params.outFile != null)
      if (!params.samFormat)
        writer = new SAMFileWriterFactory().makeBAMWriter(header, true,
            params.outFile);
      else
        writer = new SAMFileWriterFactory().makeSAMWriter(header, true,
            params.outFile);
    else if (!params.samFormat) {
      // hack to write BAM format to stdout:
      File file = File.createTempFile("bam", null);
      file.deleteOnExit();
      BAMFileWriter bamWriter = new BAMFileWriter(System.out, file);
      header.setSortOrder(SortOrder.coordinate);
      bamWriter.setHeader(header);
      writer = bamWriter;
    }


    else {

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    }


  }


  private static SAMFileHeader mergeHeaders(List<RecordSource> sources) {
    SAMFileHeader header = new SAMFileHeader();
    for (RecordSource source : sources) {
      SAMFileHeader h = source.reader.getFileHeader();


      for (SAMSequenceRecord seq : h.getSequenceDictionary()
          .getSequences()) {
        if (header.getSequenceDictionary().getSequence(
            seq.getSequenceName()) == null)
          header.addSequence(seq);
      }


      for (SAMProgramRecord pro : h.getProgramRecords()) {
        if (header.getProgramRecord(pro.getProgramGroupId()) == null)
          header.addProgramRecord(pro);
      }


      for (String comment : h.getComments())
        header.addComment(comment);


      for (SAMReadGroupRecord rg : h.getReadGroups()) {
        if (header.getReadGroup(rg.getReadGroupId()) == null)
          header.addReadGroup(rg);
      }


    }

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    return slice;
  }


  private static void randomStressTest() throws IOException,
      IllegalArgumentException, IllegalAccessException {
    SAMFileHeader samFileHeader = new SAMFileHeader();
    SAMSequenceRecord sequenceRecord = new SAMSequenceRecord("chr1", 100);
    samFileHeader.addSequence(sequenceRecord);


    long baseCount = 0;
    Random random = new Random();
    List<CramRecord> records = new ArrayList<CramRecord>();
    for (int i = 0; i < 100000; i++) {

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      // for (int i = readRecords.size() - 10; i < readRecords.size();
      // i++)
      // System.out.println(readRecords.get(i));


      time1 = System.nanoTime();
      SAMFileHeader header = Utils.cramHeader2SamHeader(cramHeader);
      List<SAMRecord> samRecords = convert(readRecords, header, null, seqName);
      for (SAMRecord r : samRecords)
        Utils.calculateMdAndNmTags(r, refBytes, true, true);
      time2 = System.nanoTime();
      System.out.printf("SAMRecords restored in in %.2f ms.\n", (time2 - time1) / 1000000f);

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Related Classes of net.sf.samtools.SAMFileHeader

abra.BetaPairValidatingRealignmentWriter

net.sf.cram.BLOCK_PROTO

net.sf.cram.Coder

net.sf.cram.Merge

net.sf.cram.ReadTag

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