Package htsjdk.samtools

Class 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 Detail

      • SAMFileWriterImpl

        public SAMFileWriterImpl()

    • Method Detail

      • 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.

      • 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.

      • 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

      • 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.

      • 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.