Package htsjdk.samtools

Class SAMFileWriterImpl

java.lang.Object
htsjdk.samtools.SAMFileWriterImpl
All Implemented Interfaces:
SAMFileWriter, Closeable, AutoCloseable
Direct Known Subclasses:
BAMFileWriter, CRAMFileWriter, SAMTextWriter
public abstract class SAMFileWriterImpl extends Object implements SAMFileWriter
Base class for implementing SAM writer with any underlying format. Mostly this manages accumulation & sorting of SAMRecords when appropriate, and produces the text version of the header, since that seems to be a popular item in both text and binary file formats.

  • Constructor Details

    • SAMFileWriterImpl

      public SAMFileWriterImpl()

  • Method Details

    • setDefaultMaxRecordsInRam

      public static void setDefaultMaxRecordsInRam(int maxRecordsInRam)
      When writing records that are not presorted, specify the number of records stored in RAM before spilling to disk. This method sets the default value for all SamFileWriterImpl instances. Must be called before the constructor is called.
      Parameters:
      maxRecordsInRam -

    • getDefaultMaxRecordsInRam

      public static int getDefaultMaxRecordsInRam()
      When writing records that are not presorted, this number determines the number of records stored in RAM before spilling to disk.
      Returns:
      DEAFULT_MAX_RECORDS_IN_RAM

    • setProgressLogger

      public void setProgressLogger(ProgressLoggerInterface progress)
      Sets the progress logger used by this implementation. Setting this lets this writer emit log messages as SAM records in a SortingCollection are being written to disk.
      Specified by:
      setProgressLogger in interface SAMFileWriter

    • setSortOrder

      public void setSortOrder(SAMFileHeader.SortOrder sortOrder, boolean presorted)
      Must be called before calling setHeader(). SortOrder value in the header passed to setHeader() is ignored. If setSortOrder is not called, default is SortOrder.unsorted.

    • setSortOrderChecking

      public void setSortOrderChecking(boolean check)
      Description copied from interface: SAMFileWriter
      If true writers that are writing pre-sorted records should check the order during writing.
      Specified by:
      setSortOrderChecking in interface SAMFileWriter

    • getSortOrder

      protected SAMFileHeader.SortOrder getSortOrder()
      Must be called after calling setHeader().

    • setMaxRecordsInRam

      protected void setMaxRecordsInRam(int maxRecordsInRam)
      When writing records that are not presorted, specify the number of records stored in RAM before spilling to disk. Must be called before setHeader().
      Parameters:
      maxRecordsInRam -

    • getMaxRecordsInRam

      protected int getMaxRecordsInRam()

    • setTempDirectory

      protected void setTempDirectory(File tmpDir)
      When writing records that are not presorted, specify the path of the temporary directory for spilling to disk. Must be called before setHeader().
      Parameters:
      tmpDir - path to the temporary directory

    • getTempDirectory

      protected File getTempDirectory()

    • setHeader

      public void setHeader(SAMFileHeader header)
      Must be called before addAlignment. Header cannot be null.

    • getFileHeader

      public SAMFileHeader getFileHeader()
      Specified by:
      getFileHeader in interface SAMFileWriter

    • addAlignment

      public void addAlignment(SAMRecord alignment)
      Add an alignment record to be emitted by the writer.
      Specified by:
      addAlignment in interface SAMFileWriter
      Parameters:
      alignment - Must not be null. The record will be updated to use the header used by this writer, which will in turn cause any unresolved reference and mate reference indices to be resolved against the header's sequence dictionary.
      Throws:
      IllegalArgumentException - if the record's reference or mate reference indices cannot be resolved against the writer's header using the current reference and mate reference names

    • close

      public final void close()
      Must be called or else file will likely be defective.
      Specified by:
      close in interface AutoCloseable
      Specified by:
      close in interface Closeable
      Specified by:
      close in interface SAMFileWriter

    • writeAlignment

      protected abstract void writeAlignment(SAMRecord alignment)
      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.
      Parameters:
      alignment -

    • writeHeader

      @Deprecated protected abstract void writeHeader(String textHeader)
      Deprecated.
      since 06/2018. writeHeader(SAMFileHeader) is preferred for avoid String construction if not need it.
      Write the header to disk. Header object is available via getHeader().
      Parameters:
      textHeader - for convenience if the implementation needs it.

    • writeHeader

      protected void writeHeader(SAMFileHeader header)
      Write the header to disk. Header object is available via getHeader().

      IMPORTANT: this method will be abstract once writeHeader(String) is removed.

      Note: default implementation uses SAMTextHeaderCodec.encode(java.io.Writer, htsjdk.samtools.SAMFileHeader) and calls writeHeader(String).

      Parameters:
      header - object to write.

    • finish

      protected abstract void finish()
      Do any required flushing here.

    • getFilename

      protected abstract String getFilename()
      For producing error messages.
      Returns:
      Output filename, or null if there isn't one.