Package htsjdk.samtools

Class BAMIndexMerger

java.lang.Object
htsjdk.samtools.IndexMerger<AbstractBAMFileIndex>
htsjdk.samtools.BAMIndexMerger
public final class BAMIndexMerger extends IndexMerger<AbstractBAMFileIndex>
Merges BAM index files for (headerless) parts of a BAM file into a single index file. The index files must have been produced using BAMIndexer with fillInUninitializedValues set to false. A partitioned BAM is a directory containing the following files:
  1. A file named header containing all header bytes in BAM format.
  2. Zero or more files named part-00000, part-00001, ... etc, containing a list of alignments in BAM format.
  3. A file named terminator containing a BGZF end-of-file marker block.
If an index is required, a BAM index can be generated for each (headerless) part file. These files should be named .part-00000.bai, .part-00001.bai, ... 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 BAM file can be created from a partitioned BAM file by concatenating all the non-hidden files (header, part-00000, part-00001, ..., terminator).
  • A BAM index can be created from a partitioned BAM file by merging all of the hidden files with a .bai suffix. Note that this is not a simple file concatenation operation. See BAMIndexMerger.

  • Constructor Details

    • BAMIndexMerger

      public BAMIndexMerger(OutputStream out, long headerLength)

  • Method Details

    • processIndex

      public void processIndex(AbstractBAMFileIndex index, long partLength)
      Description copied from class: IndexMerger
      Process the next index and add to the merged index.
      Specified by:
      processIndex in class IndexMerger<AbstractBAMFileIndex>
      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)
      Description copied from class: IndexMerger
      Finish merging the indexes, and close the output stream.
      Specified by:
      finish in class IndexMerger<AbstractBAMFileIndex>
      Parameters:
      dataFileLength - the length of the total data file, in bytes.

    • openIndex

      public static AbstractBAMFileIndex openIndex(SeekableStream stream, SAMSequenceDictionary dictionary)

    • mergeBins

      public static BinningIndexContent.BinList mergeBins(List<BinningIndexContent.BinList> binLists, long[] offsets)
      Merge bins for (headerless) BAM file parts.
      Parameters:
      binLists - the bins to merge
      offsets - bin i will be shifted by offset i
      Returns:
      the merged bins

    • mergeLinearIndexes

      public static LinearIndex mergeLinearIndexes(int referenceSequence, List<LinearIndex> linearIndexes, long[] offsets)
      Merge linear indexes for (headerless) BAM file parts.
      Parameters:
      referenceSequence - the reference sequence number for the linear indexes being merged
      linearIndexes - the linear indexes to merge
      offsets - linear index i will be shifted by offset i
      Returns:
      the merged linear index