Field Detail

• BAM_FILE_EXTENSION

  public static final String BAM_FILE_EXTENSION

  See Also:

  Constant Field Values

Constructor Detail

• BamFileIoUtils

  public BamFileIoUtils()

Method Detail

• isBamFile

  public static boolean isBamFile(File file)

• reheaderBamFile

  public static void reheaderBamFile(SAMFileHeader samFileHeader,
                                     File inputFile,
                                     File outputFile)

• reheaderBamFile

  public static void reheaderBamFile(SAMFileHeader samFileHeader,
                                     File inputFile,
                                     File outputFile,
                                     boolean createMd5,
                                     boolean createIndex)

  Copy a BAM file but replacing the header

  Parameters:

  samFileHeader - The header to use in the new file

  inputFile - The BAM file to copy, sans header

  outputFile - The new BAM file, constructed with the new header and the content from inputFile

  createMd5 - Whether or not to create an MD5 file for the new BAM

  createIndex - Whether or not to create an index file for the new BAM

• blockCopyBamFile

  public static void blockCopyBamFile(File inputFile,
                                      OutputStream outputStream,
                                      boolean skipHeader,
                                      boolean skipTerminator)

  Copy data from a BAM file to an OutputStream by directly copying the gzip blocks

  Parameters:

  inputFile - The file to be copied

  outputStream - The stream to write the copied data to

  skipHeader - If true, the header of the input file will not be copied to the output stream

  skipTerminator - If true, the terminator block of the input file will not be written to the output stream

• gatherWithBlockCopying

  public static void gatherWithBlockCopying(List<File> bams,
                                            File output,
                                            boolean createIndex,
                                            boolean createMd5)

  Assumes that all inputs and outputs are block compressed VCF files and copies them without decompressing and parsing most of the gzip blocks. Will decompress and parse blocks up to the one containing the end of the header in each file (often the first block) and re-compress any data remaining in that block into a new block in the output file. Subsequent blocks (excluding a terminator block if present) are copied directly from input to output.