Class SamPairUtil

java.lang.Object
htsjdk.samtools.SamPairUtil
public class SamPairUtil extends Object
Utility methods for pairs of SAMRecords

  • Constructor Details

    • SamPairUtil

      public SamPairUtil()

  • Method Details

    • getPairOrientation

      public static SamPairUtil.PairOrientation getPairOrientation(SAMRecord record)
      Computes the pair orientation of the given SAMRecord.
      Parameters:
      record - the record for which the pair orientation is requested
      Returns:
      PairOrientation of the given SAMRecord.
      Throws:
      IllegalArgumentException - If the record is not a paired read, or one or both reads are unmapped, or if the two records are not mapped to the same reference. NOTA BENE: This is NOT the orientation byte as used in Picard's MarkDuplicates. For that please look in ReadEnds (in Picard). When the record is on the forward strand, the mate's 5' position is computed from the mate CIGAR (MC) tag if present, and otherwise falls back to CoordMath.getEnd(getAlignmentStart(), getInferredInsertSize()). The fallback is exact for TLEN values written under htsjdk's 5'-to-5' convention (see computeInsertSize(SAMRecord, SAMRecord)) but can still produce asymmetric results on dovetail pairs when TLEN was written under SAM v1 ยง1.4's leftmost-to-rightmost convention. Callers that need symmetric orientation on such pairs should ensure the MC tag is set on at least the forward-strand record.

    • isProperPair

      public static boolean isProperPair(SAMRecord firstEnd, SAMRecord secondEnd, List<SamPairUtil.PairOrientation> expectedOrientations)

    • assertMate

      public static void assertMate(SAMRecord firstOfPair, SAMRecord secondOfPair)

    • obtainAssertedMate

      public static SAMRecord obtainAssertedMate(Iterator<SAMRecord> samRecordIterator, SAMRecord firstOfPair)
      Obtain the secondOfPair mate belonging to the firstOfPair SAMRecord (assumed to be in the next element of the specified samRecordIterator)
      Parameters:
      samRecordIterator - the iterator assumed to contain the secondOfPair SAMRecord in the next element in the iteration
      firstOfPair - the firstOfPair SAMRecord
      Returns:
      the secondOfPair SAMRecord
      Throws:
      SAMException - when the secondOfPair mate cannot be obtained due to assertion failures

    • computeInsertSize

      public static int computeInsertSize(SAMRecord firstEnd, SAMRecord secondEnd)
      Compute SAMRecord insert size
      Parameters:
      firstEnd -
      secondEnd -
      Returns:
      note that when storing insert size on the secondEnd, the return value must be negated.

    • setMateInfo

      public static void setMateInfo(SAMRecord rec1, SAMRecord rec2)
      Write the mate info for two SAMRecords. This will always clear/remove any mate cigar tag that is present.
      Parameters:
      rec1 - the first SAM record
      rec2 - the second SAM record

    • setMateInfo

      public static void setMateInfo(SAMRecord rec1, SAMRecord rec2, boolean setMateCigar)
      Write the mate info for two SAMRecords
      Parameters:
      rec1 - the first SAM record. Must have a non-null SAMFileHeader.
      rec2 - the second SAM record. Must have a non-null SAMFileHeader.
      setMateCigar - true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.

    • setMateInfo

      @Deprecated public static void setMateInfo(SAMRecord rec1, SAMRecord rec2, SAMFileHeader header, boolean setMateCigar)
      Deprecated.
      use setMateInfo(SAMRecord, SAMRecord, boolean) instead
      Write the mate info for two SAMRecords
      Parameters:
      rec1 - the first SAM record
      rec2 - the second SAM record
      header - the SAM file header
      setMateCigar - true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.

    • setMateInfo

      @Deprecated public static void setMateInfo(SAMRecord rec1, SAMRecord rec2, SAMFileHeader header)
      Deprecated.
      use setMateInfo(SAMRecord, SAMRecord) instead
      Write the mate info for two SAMRecords. This will always clear/remove any mate cigar tag that is present.
      Parameters:
      rec1 - the first SAM record
      rec2 - the second SAM record
      header - the SAM file header

    • setMateInformationOnSupplementalAlignment

      public static void setMateInformationOnSupplementalAlignment(SAMRecord supplemental, SAMRecord matePrimary, boolean setMateCigar)
      Sets mate pair information appropriately on a supplemental SAMRecord (e.g. from a split alignment) using the primary alignment of the read's mate.
      Parameters:
      supplemental - a supplemental alignment for the mate pair of the primary supplied
      matePrimary - the primary alignment of the the mate pair of the supplemental
      setMateCigar - true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.

    • setMateInformationOnSupplementalAlignment

      public static void setMateInformationOnSupplementalAlignment(SAMRecord supplemental, SAMRecord matePrimary)
      Sets mate pair information appropriately on a supplemental SAMRecord (e.g. from a split alignment) using the primary alignment of the read's mate.
      Parameters:
      supplemental - a supplemental alignment for the mate pair of the primary supplied
      matePrimary - the primary alignment of the the mate pair of the supplemental

    • setProperPairAndMateInfo

      @Deprecated public static void setProperPairAndMateInfo(SAMRecord rec1, SAMRecord rec2, SAMFileHeader header, List<SamPairUtil.PairOrientation> expectedOrientations)
      Deprecated.
      use setProperPairAndMateInfo(SAMRecord, SAMRecord, List) instead
      This method will clear any mate cigar already present.

    • setProperPairAndMateInfo

      @Deprecated public static void setProperPairAndMateInfo(SAMRecord rec1, SAMRecord rec2, SAMFileHeader header, List<SamPairUtil.PairOrientation> expectedOrientations, boolean addMateCigar)
      Deprecated.
      use setProperPairAndMateInfo(SAMRecord, SAMRecord, List, boolean)
      Parameters:
      addMateCigar - true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.

    • setProperPairAndMateInfo

      public static void setProperPairAndMateInfo(SAMRecord rec1, SAMRecord rec2, List<SamPairUtil.PairOrientation> expectedOrientations)
      This method will clear any mate cigar already present.

    • setProperPairAndMateInfo

      public static void setProperPairAndMateInfo(SAMRecord rec1, SAMRecord rec2, List<SamPairUtil.PairOrientation> expectedOrientations, boolean addMateCigar)
      Parameters:
      addMateCigar - true if we are to update/create the Mate CIGAR (MC) optional tag, false if we are to clear any mate cigar tag that is present.

    • setProperPairFlags

      public static void setProperPairFlags(SAMRecord rec1, SAMRecord rec2, List<SamPairUtil.PairOrientation> expectedOrientations)