Package htsjdk.samtools

Class SamPairUtil

  • public class SamPairUtil
extends Object
    Utility methods for pairs of SAMRecords

    • Constructor Detail

      • SamPairUtil

        public SamPairUtil()

    • Method Detail

      • getPairOrientation

        public static SamPairUtil.PairOrientation getPairOrientation​(SAMRecord r)
        Computes the pair orientation of the given SAMRecord.
        Parameters:
        r -
        Returns:
        PairOrientation of the given SAMRecord.
        Throws:
        IllegalArgumentException - If the record is not a paired read, or one or both reads are unmapped.

      • 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

        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.