Package htsjdk.samtools

Class SamFileHeaderMerger

java.lang.Object
htsjdk.samtools.SamFileHeaderMerger
public class SamFileHeaderMerger extends Object
Merges SAMFileHeaders that have the same sequences into a single merged header object while providing read group translation for cases where read groups clash across input headers.

  • Constructor Details

    • SamFileHeaderMerger

      @Deprecated public SamFileHeaderMerger(Collection<SamReader> readers, SAMFileHeader.SortOrder sortOrder)
      Deprecated.
      replaced by SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)
      Create SAMFileHeader with additional information. Required that sequence dictionaries agree.
      Parameters:
      readers - sam file readers to combine
      sortOrder - sort order new header should have

    • SamFileHeaderMerger

      @Deprecated public SamFileHeaderMerger(Collection<SamReader> readers, SAMFileHeader.SortOrder sortOrder, boolean mergeDictionaries)
      Deprecated.
      replaced by SamFileHeaderMerger(SAMFileHeader.SortOrder, Collection, boolean)
      Create SAMFileHeader with additional information.
      Parameters:
      readers - sam file readers to combine
      sortOrder - sort order new header should have
      mergeDictionaries - If true, merge sequence dictionaries in new header. If false, require that all input sequence dictionaries be identical.

    • SamFileHeaderMerger

      public SamFileHeaderMerger(SAMFileHeader.SortOrder sortOrder, Collection<SAMFileHeader> headers, boolean mergeDictionaries)
      Create SAMFileHeader with additional information.. This is the preferred constructor.
      Parameters:
      sortOrder - sort order new header should have
      headers - sam file headers to combine
      mergeDictionaries - If true, merge sequence dictionaries in new header. If false, require that all input sequence dictionaries be identical.

  • Method Details

    • positiveFourDigitBase36Str

      public static String positiveFourDigitBase36Str(int leftOver)
      Convert an integer to base36, protected solely for testing
      Parameters:
      leftOver - Both the initial value and the running quotient
      Returns:
      A four digit string composed of base 36 symbols

    • getReadGroupId

      @Deprecated public String getReadGroupId(SamReader reader, String originalReadGroupId)
      Deprecated.
      replaced by getReadGroupId(SAMFileHeader, String)
      Returns the read group id that should be used for the input read and RG id.

    • getReadGroupId

      public String getReadGroupId(SAMFileHeader header, String originalReadGroupId)
      Returns the read group id that should be used for the input read and RG id.

    • getProgramGroupId

      @Deprecated public String getProgramGroupId(SamReader reader, String originalProgramGroupId)
      Deprecated.
      replaced by getProgramGroupId(SAMFileHeader, String)
      Parameters:
      reader - one of the input files
      originalProgramGroupId - a program group ID from the above input file
      Returns:
      new ID from the merged list of program groups in the output file

    • getProgramGroupId

      public String getProgramGroupId(SAMFileHeader header, String originalProgramGroupId)
      Parameters:
      header - one of the input headers
      originalProgramGroupId - a program group ID from the above input file
      Returns:
      new ID from the merged list of program groups in the output file

    • hasReadGroupCollisions

      public boolean hasReadGroupCollisions()
      Returns true if there are read group duplicates within the merged headers.

    • hasProgramGroupCollisions

      public boolean hasProgramGroupCollisions()
      Returns true if there are program group duplicates within the merged headers.

    • hasMergedSequenceDictionary

      public boolean hasMergedSequenceDictionary()
      Returns:
      if we've merged the sequence dictionaries, return true

    • getMergedHeader

      public SAMFileHeader getMergedHeader()
      Returns the merged header that should be written to any output merged file.

    • getReaders

      @Deprecated public Collection<SamReader> getReaders()
      Deprecated.
      replaced by getHeaders()
      Returns the collection of readers that this header merger is working with. May return null.

    • getHeaders

      public Collection<SAMFileHeader> getHeaders()
      Returns the collection of readers that this header merger is working with.

    • getMergedSequenceIndex

      @Deprecated public Integer getMergedSequenceIndex(SamReader reader, Integer oldReferenceSequenceIndex)
      Deprecated.
      replaced by getMergedSequenceIndex(SAMFileHeader, Integer)
      returns the new mapping for a specified reader, given it's old sequence index
      Parameters:
      reader - the reader
      oldReferenceSequenceIndex - the old sequence (also called reference) index
      Returns:
      the new index value

    • getMergedSequenceIndex

      public Integer getMergedSequenceIndex(SAMFileHeader header, Integer oldReferenceSequenceIndex)
      Another mechanism for getting the new sequence index, for situations in which the reader is not available. Note that if the SAMRecord has already had its header replaced with the merged header, this won't work.
      Parameters:
      header - The original header for the input record in question.
      oldReferenceSequenceIndex - The original sequence index.
      Returns:
      the new index value that is compatible with the merged sequence index.