@Deprecated
public class SAMRecordUtil
extends java.lang.Object
SAMRecord.reverseComplement()
instead, which defaults to making a copy of attributes for reverse
complement rather than changing them in-place.Modifier and Type | Field and Description |
---|---|
static java.util.List<java.lang.String> |
TAGS_TO_REVERSE
Deprecated.
|
static java.util.List<java.lang.String> |
TAGS_TO_REVERSE_COMPLEMENT
Deprecated.
|
Constructor and Description |
---|
SAMRecordUtil()
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
static void |
reverseComplement(SAMRecord rec)
Deprecated.
Reverse-complement bases and reverse quality scores along with known optional attributes that
need the same treatment.
|
static void |
reverseComplement(SAMRecord rec,
boolean inplace)
Deprecated.
Reverse-complement bases and reverse quality scores along with known optional attributes that
need the same treatment.
|
static void |
reverseComplement(SAMRecord rec,
java.util.Collection<java.lang.String> tagsToRevcomp,
java.util.Collection<java.lang.String> tagsToReverse,
boolean inplace)
Deprecated.
Reverse complement bases and reverse quality scores.
|
public static java.util.List<java.lang.String> TAGS_TO_REVERSE_COMPLEMENT
public static java.util.List<java.lang.String> TAGS_TO_REVERSE
public static void reverseComplement(SAMRecord rec)
reverseComplement(SAMRecord, boolean)
.
See TAGS_TO_REVERSE_COMPLEMENT
TAGS_TO_REVERSE
for the default set of tags that are handled.public static void reverseComplement(SAMRecord rec, boolean inplace)
TAGS_TO_REVERSE_COMPLEMENT
TAGS_TO_REVERSE
for the default set of tags that are handled.rec
- Record to reverse complement.inplace
- Setting this to false will clone all attributes, bases and qualities before changing the values.public static void reverseComplement(SAMRecord rec, java.util.Collection<java.lang.String> tagsToRevcomp, java.util.Collection<java.lang.String> tagsToReverse, boolean inplace)