htsjdk.samtools

Class SamPairUtil

java.lang.Object

htsjdk.samtools.SamPairUtil

public class SamPairUtil
extends java.lang.Object

Utility methods for pairs of SAMRecords

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SamPairUtil.PairOrientation The possible orientations of paired reads.
static class	SamPairUtil.SetMateInfoIterator A class to iterate through SAMRecords and set mate information on the given records, and optionally set the mate cigar tag (true by default).

Constructor Summary

Constructors

Constructor and Description
SamPairUtil()

Method Summary

Methods

Modifier and Type	Method and Description
static void	assertMate(SAMRecord firstOfPair, SAMRecord secondOfPair)
static int	computeInsertSize(SAMRecord firstEnd, SAMRecord secondEnd) Compute SAMRecord insert size
static SamPairUtil.PairOrientation	getPairOrientation(SAMRecord r) Computes the pair orientation of the given SAMRecord.
static boolean	isProperPair(SAMRecord firstEnd, SAMRecord secondEnd, java.util.List<SamPairUtil.PairOrientation> expectedOrientations)
static SAMRecord	obtainAssertedMate(java.util.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)
static void	setMateInfo(SAMRecord rec1, SAMRecord rec2, boolean setMateCigar) Write the mate info for two SAMRecords
static void	setMateInfo(SAMRecord rec1, SAMRecord rec2, SAMFileHeader header) Write the mate info for two SAMRecords.
static void	setMateInfo(SAMRecord rec1, SAMRecord rec2, SAMFileHeader header, boolean setMateCigar) Deprecated.
static void	setMateInformationOnSupplementalAlignment(SAMRecord supplemental, SAMRecord matePrimary) Sets mate pair information appropriately on a supplemental SAMRecord (e.g.
static void	setMateInformationOnSupplementalAlignment(SAMRecord supplemental, SAMRecord matePrimary, boolean setMateCigar) Sets mate pair information appropriately on a supplemental SAMRecord (e.g.
static void	setProperPairAndMateInfo(SAMRecord rec1, SAMRecord rec2, SAMFileHeader header, java.util.List<SamPairUtil.PairOrientation> exepectedOrientations) This method will clear any mate cigar already present.
static void	setProperPairAndMateInfo(SAMRecord rec1, SAMRecord rec2, SAMFileHeader header, java.util.List<SamPairUtil.PairOrientation> exepectedOrientations, boolean addMateCigar)
static void	setProperPairFlags(SAMRecord rec1, SAMRecord rec2, java.util.List<SamPairUtil.PairOrientation> expectedOrientations)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

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:

java.lang.IllegalArgumentException - If the record is not a paired read, or one or both reads are unmapped.

isProperPair

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

assertMate

public static void assertMate(SAMRecord firstOfPair,
              SAMRecord secondOfPair)

obtainAssertedMate

public static SAMRecord obtainAssertedMate(java.util.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,
               boolean setMateCigar)

Write the mate info for two SAMRecords

Parameters:

rec1 - the first SAM record

rec2 - the second SAM record

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.

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

public static void setMateInfo(SAMRecord rec1,
               SAMRecord rec2,
               SAMFileHeader header)

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,
                            SAMFileHeader header,
                            java.util.List<SamPairUtil.PairOrientation> exepectedOrientations)

This method will clear any mate cigar already present.

setProperPairAndMateInfo

public static void setProperPairAndMateInfo(SAMRecord rec1,
                            SAMRecord rec2,
                            SAMFileHeader header,
                            java.util.List<SamPairUtil.PairOrientation> exepectedOrientations,
                            boolean addMateCigar)

Parameters:

rec1 -

rec2 -

header -

exepectedOrientations -

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,
                      java.util.List<SamPairUtil.PairOrientation> expectedOrientations)