Package htsjdk.samtools

Class BAMFileWriter

java.lang.Object
htsjdk.samtools.SAMFileWriterImpl
htsjdk.samtools.BAMFileWriter
All Implemented Interfaces:
SAMFileWriter, Closeable, AutoCloseable
public class BAMFileWriter extends SAMFileWriterImpl
Concrete implementation of SAMFileWriter for writing gzipped BAM files.

  • Constructor Details

    • BAMFileWriter

      protected BAMFileWriter(File path)

    • BAMFileWriter

      protected BAMFileWriter(File path, int compressionLevel)

    • BAMFileWriter

      protected BAMFileWriter(OutputStream os, File file)

    • BAMFileWriter

      protected BAMFileWriter(OutputStream os, File file, int compressionLevel)

    • BAMFileWriter

      protected BAMFileWriter(OutputStream os, File file, int compressionLevel, DeflaterFactory deflaterFactory)

    • BAMFileWriter

      protected BAMFileWriter(OutputStream os, String absoluteFilename, int compressionLevel, DeflaterFactory deflaterFactory)

  • Method Details

    • 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
      Parameters:
      alignment -

    • 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.

    • finish

      protected void finish()
      Description copied from class: SAMFileWriterImpl
      Do any required flushing here.
      Specified by:
      finish in class SAMFileWriterImpl

    • 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.

    • 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