Class BAMFileWriter

    • Constructor Detail

      • BAMFileWriter

        protected BAMFileWriter​(File path)
      • BAMFileWriter

        protected BAMFileWriter​(File path,
                                int compressionLevel)
      • BAMFileWriter

        protected BAMFileWriter​(OutputStream os,
                                File file,
                                int compressionLevel)
    • Method Detail

      • writeAlignment

        protected void writeAlignment​(SAMRecord alignment)
        Description copied from class: SAMFileWriterImpl
        Writes the record to disk. Sort order has been taken care of by the time this method is called. The record must hava a non-null SAMFileHeader.
        Specified by:
        writeAlignment in class SAMFileWriterImpl
      • writeHeader

        protected void writeHeader​(String textHeader)
        Description copied from class: SAMFileWriterImpl
        Write the header to disk. Header object is available via getHeader().
        Specified by:
        writeHeader in class SAMFileWriterImpl
        Parameters:
        textHeader - for convenience if the implementation needs it.
      • getFilename

        protected String getFilename()
        Description copied from class: SAMFileWriterImpl
        For producing error messages.
        Specified by:
        getFilename in class SAMFileWriterImpl
        Returns:
        absolute path in URI format, or null if this writer does not correspond to a file. To get a Path from this, use: IOUtil.getPath(getFilename())
      • writeHeader

        protected static void writeHeader​(BinaryCodec outputBinaryCodec,
                                          SAMFileHeader samFileHeader,
                                          String headerText)
        Writes a header to a BAM file. samFileHeader and headerText are redundant - one can be used to regenerate the other but in some instances we already have both so this allows us to save some cycles
      • writeHeader

        protected static void writeHeader​(BinaryCodec outputBinaryCodec,
                                          SAMFileHeader samFileHeader)
        Writes a header to a BAM file. Might need to regenerate the String version of the header, if one already has both the samFileHeader and the String, use the version of this method which takes both.
      • writeHeader

        public static void writeHeader​(OutputStream outputStream,
                                       SAMFileHeader samFileHeader)
        Write a BAM file header to an output stream in block compressed BAM format.
        Parameters:
        outputStream - the stream to write the BAM header to
        samFileHeader - the header to write