Examples of CRAMIndexer

net.sf.samtools.CRAMIndexer
Class for both constructing BAM index content and writing it out. There are two usage patterns: 1) Building a bam index from an existing bam file 2) Building a bam index while building the bam file In both cases, processAlignment is called for each alignment record and finish() is called at the end.

Examples of net.sf.samtools.CRAMIndexer


  public BaiIndexer(InputStream is, SAMFileHeader samFileHeader, File output) {
    this.is = new CountingInputStream(is);
    this.samFileHeader = samFileHeader;


    indexer = new CRAMIndexer(output, samFileHeader);
  }

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Examples of net.sf.samtools.CRAMIndexer

  public BaiIndexer(InputStream is, File output) throws IOException {
    this.is = new CountingInputStream(is);
    CramHeader cramHeader = ReadWrite.readCramHeader(this.is);
    samFileHeader = cramHeader.samFileHeader;


    indexer = new CRAMIndexer(output, samFileHeader);
  }

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