Package htsjdk.samtools

Class CRAMBAIIndexer

java.lang.Object
htsjdk.samtools.CRAMBAIIndexer
All Implemented Interfaces:
CRAMIndexer
public class CRAMBAIIndexer extends Object implements CRAMIndexer
Class for both constructing BAM index content and writing it out. There are two usage patterns: 1) Building a bam index (BAI) while building the CRAM file 2) Building a bam index (BAI) from an existing CRAI file 1) is driven by CRAMContainerStreamWriter and proceeds by calling processContainer(htsjdk.samtools.cram.structure.Container, htsjdk.samtools.ValidationStringency) after each Container is built, and finish() is called at the end. 2) is driven by CRAIIndex.openCraiFileAsBaiStream(InputStream, SAMSequenceDictionary) and proceeds by processing CRAIEntry elements obtained from CRAMCRAIIndexer.readIndex(InputStream). processBAIEntry(BAIEntry) is called on each CRAIEntry and finish() is called at the end. NOTE: a third pattern of building a BAI from a CRAM file is also supported by this class, but it is unused. This would be accomplished via createIndex(SeekableStream, File, Log, ValidationStringency).

  • Constructor Details

    • CRAMBAIIndexer

      public CRAMBAIIndexer(OutputStream output, SAMFileHeader fileHeader)
      Create a CRAM indexer that writes BAI to a stream.
      Parameters:
      output - Index will be written here. output will be closed when finish() method is called.
      fileHeader - header for the corresponding bam file.

  • Method Details

    • processContainer

      public void processContainer(Container container, ValidationStringency validationStringency)
      Index a container, any of mapped, unmapped and multiple references are allowed. The only requirement is sort order by coordinate. For multiref containers the method reads the container through unpacking all reads. This is slower than single reference but should be faster than normal reading.
      Specified by:
      processContainer in interface CRAMIndexer
      Parameters:
      container - container to be indexed
      validationStringency - stringency for validating records (used when processing multi-reference slices, since creating an index on a multi-ref slices requires actually decoding the records in order to resove the constituent reference spans}

    • processBAIEntry

      public final void processBAIEntry(BAIEntry baiEntry)

    • finish

      public void finish()
      After all the slices have been processed, finish is called. Writes any final information and closes the output file.
      Specified by:
      finish in interface CRAMIndexer

    • createIndex

      public static void createIndex(SeekableStream stream, File output, Log log, ValidationStringency validationStringency)
      Generates a BAI index file from an input CRAM stream
      Parameters:
      stream - CRAM stream to index
      output - File for output index file
      log - optional Log to output progress