Package htsjdk.samtools

Class SAMTextWriter

java.lang.Object
htsjdk.samtools.SAMFileWriterImpl
htsjdk.samtools.SAMTextWriter
All Implemented Interfaces:
SAMFileWriter, Closeable, AutoCloseable
public class SAMTextWriter extends SAMFileWriterImpl
Writer for text-format SAM files.

  • Constructor Details

    • SAMTextWriter

      public SAMTextWriter(Writer out)
      Constructs a SAMTextWriter that outputs to a Writer.
      Parameters:
      out - Writer.

    • SAMTextWriter

      public SAMTextWriter(File file)
      Constructs a SAMTextWriter that writes to a File.
      Parameters:
      file - Where to write the output.

    • SAMTextWriter

      public SAMTextWriter(OutputStream stream)
      Constructs a SAMTextWriter that writes to an OutputStream. The OutputStream is wrapped in an AsciiWriter, which can be retrieved with getWriter().
      Parameters:
      stream - Need not be buffered because this class provides buffering.

    • SAMTextWriter

      public SAMTextWriter(Writer out, SamFlagField samFlagFieldOutput)
      Constructs a SAMTextWriter that outputs to a Writer.
      Parameters:
      out - Writer.

    • SAMTextWriter

      public SAMTextWriter(File file, SamFlagField samFlagFieldOutput)
      Constructs a SAMTextWriter that writes to a File.
      Parameters:
      file - Where to write the output.

    • SAMTextWriter

      public SAMTextWriter(OutputStream stream, SamFlagField samFlagFieldOutput)
      Constructs a SAMTextWriter that writes to an OutputStream. The OutputStream is wrapped in an AsciiWriter, which can be retrieved with getWriter().
      Parameters:
      stream - Need not be buffered because this class provides buffering.

  • Method Details