public class SamPairUtil
extends java.lang.Object
Modifier and Type | Class and Description |
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static class |
SamPairUtil.PairOrientation
The possible orientations of paired reads.
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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 and Description |
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SamPairUtil() |
Modifier and Type | Method and Description |
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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)
Write the mate info for two SAMRecords.
|
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)
Deprecated.
use
setMateInfo(SAMRecord, SAMRecord) instead |
static void |
setMateInfo(SAMRecord rec1,
SAMRecord rec2,
SAMFileHeader header,
boolean setMateCigar)
Deprecated.
use
setMateInfo(SAMRecord, SAMRecord, boolean) instead |
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,
java.util.List<SamPairUtil.PairOrientation> expectedOrientations)
This method will clear any mate cigar already present.
|
static void |
setProperPairAndMateInfo(SAMRecord rec1,
SAMRecord rec2,
java.util.List<SamPairUtil.PairOrientation> expectedOrientations,
boolean addMateCigar) |
static void |
setProperPairAndMateInfo(SAMRecord rec1,
SAMRecord rec2,
SAMFileHeader header,
java.util.List<SamPairUtil.PairOrientation> expectedOrientations)
Deprecated.
|
static void |
setProperPairAndMateInfo(SAMRecord rec1,
SAMRecord rec2,
SAMFileHeader header,
java.util.List<SamPairUtil.PairOrientation> expectedOrientations,
boolean addMateCigar)
Deprecated.
|
static void |
setProperPairFlags(SAMRecord rec1,
SAMRecord rec2,
java.util.List<SamPairUtil.PairOrientation> expectedOrientations) |
public static SamPairUtil.PairOrientation getPairOrientation(SAMRecord r)
r
- java.lang.IllegalArgumentException
- If the record is not a paired read, or
one or both reads are unmapped.public static boolean isProperPair(SAMRecord firstEnd, SAMRecord secondEnd, java.util.List<SamPairUtil.PairOrientation> expectedOrientations)
public static SAMRecord obtainAssertedMate(java.util.Iterator<SAMRecord> samRecordIterator, SAMRecord firstOfPair)
samRecordIterator
- the iterator assumed to contain the secondOfPair SAMRecord in the
next element in the iterationfirstOfPair
- the firstOfPair SAMRecordSAMException
- when the secondOfPair mate cannot be obtained due to assertion failurespublic static int computeInsertSize(SAMRecord firstEnd, SAMRecord secondEnd)
firstEnd
- secondEnd
- public static void setMateInfo(SAMRecord rec1, SAMRecord rec2)
rec1
- the first SAM recordrec2
- the second SAM recordpublic static void setMateInfo(SAMRecord rec1, SAMRecord rec2, boolean setMateCigar)
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.@Deprecated public static void setMateInfo(SAMRecord rec1, SAMRecord rec2, SAMFileHeader header, boolean setMateCigar)
setMateInfo(SAMRecord, SAMRecord, boolean)
insteadrec1
- the first SAM recordrec2
- the second SAM recordheader
- the SAM file headersetMateCigar
- 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.@Deprecated public static void setMateInfo(SAMRecord rec1, SAMRecord rec2, SAMFileHeader header)
setMateInfo(SAMRecord, SAMRecord)
insteadrec1
- the first SAM recordrec2
- the second SAM recordheader
- the SAM file headerpublic static void setMateInformationOnSupplementalAlignment(SAMRecord supplemental, SAMRecord matePrimary, boolean setMateCigar)
supplemental
- a supplemental alignment for the mate pair of the primary suppliedmatePrimary
- the primary alignment of the the mate pair of the supplementalsetMateCigar
- 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.public static void setMateInformationOnSupplementalAlignment(SAMRecord supplemental, SAMRecord matePrimary)
supplemental
- a supplemental alignment for the mate pair of the primary suppliedmatePrimary
- the primary alignment of the the mate pair of the supplemental@Deprecated public static void setProperPairAndMateInfo(SAMRecord rec1, SAMRecord rec2, SAMFileHeader header, java.util.List<SamPairUtil.PairOrientation> expectedOrientations)
setProperPairAndMateInfo(SAMRecord, SAMRecord, List)
instead@Deprecated public static void setProperPairAndMateInfo(SAMRecord rec1, SAMRecord rec2, SAMFileHeader header, java.util.List<SamPairUtil.PairOrientation> expectedOrientations, boolean addMateCigar)
setProperPairAndMateInfo(SAMRecord, SAMRecord, List, boolean)
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.public static void setProperPairAndMateInfo(SAMRecord rec1, SAMRecord rec2, java.util.List<SamPairUtil.PairOrientation> expectedOrientations)
public static void setProperPairAndMateInfo(SAMRecord rec1, SAMRecord rec2, java.util.List<SamPairUtil.PairOrientation> expectedOrientations, boolean addMateCigar)
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.public static void setProperPairFlags(SAMRecord rec1, SAMRecord rec2, java.util.List<SamPairUtil.PairOrientation> expectedOrientations)