Package htsjdk.samtools.cram

Class CRAIIndexMerger

java.lang.Object
htsjdk.samtools.IndexMerger<CRAIIndex>
htsjdk.samtools.cram.CRAIIndexMerger
public final class CRAIIndexMerger extends IndexMerger<CRAIIndex>
Merges CRAM index files for (headerless) parts of a CRAM file into a single index file. A partitioned CRAM is a directory containing the following files:
  1. A file named header containing all header bytes (CRAM header and CRAM container containing the BAM header).
  2. Zero or more files named part-00000, part-00001, ... etc, containing CRAM containers.
  3. A file named terminator containing a CRAM end-of-file marker container.
If an index is required, a CRAM index can be generated for each (headerless) part file. These files should be named .part-00000.crai, .part-00001.crai, ... etc. Note the leading . to make the files hidden. This format has the following properties:
  • Parts and their indexes may be written in parallel, since one part file can be written independently of the others.
  • A CRAM file can be created from a partitioned CRAM file by merging all the non-hidden files (header, part-00000, part-00001, ..., terminator).
  • A CRAM index can be created from a partitioned CRAM file by merging all of the hidden files with a .crai suffix. Note that this is not a simple file concatenation operation. See CRAIIndexMerger.

  • Constructor Details

  • Method Details

    • processIndex

      public void processIndex(CRAIIndex index, long partLength)
      Description copied from class: IndexMerger
      Process the next index and add to the merged index.
      Specified by:
      processIndex in class IndexMerger<CRAIIndex>
      Parameters:
      index - the index to merge
      partLength - the length of the part file corresponding to the index, in bytes.

    • finish

      public void finish(long dataFileLength) throws IOException
      Description copied from class: IndexMerger
      Finish merging the indexes, and close the output stream.
      Specified by:
      finish in class IndexMerger<CRAIIndex>
      Parameters:
      dataFileLength - the length of the total data file, in bytes.
      Throws:
      IOException - if an error occurs