htsjdk.samtools

Class SAMRecordUtil

java.lang.Object

htsjdk.samtools.SAMRecordUtil

Deprecated.

@Deprecated
public class SAMRecordUtil
extends java.lang.Object

Use SAMRecord.reverseComplement() instead, which defaults to making a copy of attributes for reverse complement rather than changing them in-place.

Field Summary

Fields

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 Summary

Constructors

Constructor and Description
SAMRecordUtil() Deprecated.

Method Summary

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.

Methods inherited from class java.lang.Object

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

Field Detail

TAGS_TO_REVERSE_COMPLEMENT

public static java.util.List<java.lang.String> TAGS_TO_REVERSE_COMPLEMENT

Deprecated.

TAGS_TO_REVERSE

public static java.util.List<java.lang.String> TAGS_TO_REVERSE

Deprecated.

Constructor Detail

SAMRecordUtil

public SAMRecordUtil()

Deprecated.

Method Detail

reverseComplement

public static void reverseComplement(SAMRecord rec)

Deprecated.

Reverse-complement bases and reverse quality scores along with known optional attributes that need the same treatment. Changes made in-place, instead of making a copy of the bases, qualities, or attributes. If a copy is needed use reverseComplement(SAMRecord, boolean). See TAGS_TO_REVERSE_COMPLEMENT TAGS_TO_REVERSE for the default set of tags that are handled.

reverseComplement

public 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. Optionally makes a copy of the bases, qualities or attributes instead of altering them in-place. See TAGS_TO_REVERSE_COMPLEMENT TAGS_TO_REVERSE for the default set of tags that are handled.

Parameters:

rec - Record to reverse complement.

inplace - Setting this to false will clone all attributes, bases and qualities before changing the values.

reverseComplement

public 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. In addition reverse complement any non-null attributes specified by tagsToRevcomp and reverse and non-null attributes specified by tagsToReverse.