Package htsjdk.samtools

Interface SAMFileWriter

All Superinterfaces:
AutoCloseable, Closeable
All Known Implementing Classes:
BAMFileWriter, CRAMFileWriter, SAMFileWriterImpl, SAMTextWriter
public interface SAMFileWriter extends Closeable
Interface for SAMText and BAM file writers. Clients need not care which they write to, once the object is constructed.

  • Method Details

    • addAlignment

      void addAlignment(SAMRecord alignment)

    • getFileHeader

      SAMFileHeader getFileHeader()

    • setProgressLogger

      void setProgressLogger(ProgressLoggerInterface progress)
      Sets a ProgressLogger on this writer. This is useful when pulling, for instance, from a SortingCollection.

    • setSortOrderChecking

      default void setSortOrderChecking(boolean check)
      If true writers that are writing pre-sorted records should check the order during writing.

    • close

      void close()
      Must be called to flush or file will likely be defective.
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable