SAMRecordUtil (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.samtools.SAMRecordUtil

Deprecated.
```
@Deprecated
public class SAMRecordUtil
extends 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 List<String> TAGS_TO_REVERSE
Deprecated.

static List<String> TAGS_TO_REVERSE_COMPLEMENT
Deprecated.

Fields
Modifier and Type	Field and Description
`static List<String>`	`TAGS_TO_REVERSE` Deprecated.
`static List<String>`	`TAGS_TO_REVERSE_COMPLEMENT` Deprecated.

Constructor Summary

Constructors
Constructor and Description

SAMRecordUtil()
Deprecated.

Constructors
Constructor and Description
`SAMRecordUtil()` Deprecated.

Method Summary

All Methods Static Methods Concrete Methods Deprecated Methods
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, Collection<String> tagsToRevcomp, Collection<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 List<String> TAGS_TO_REVERSE_COMPLEMENT
```
    Deprecated.
  - TAGS_TO_REVERSE
```
public static List<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,
                                     Collection<String> tagsToRevcomp,
                                     Collection<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.

Class SAMRecordUtil

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

TAGS_TO_REVERSE_COMPLEMENT

TAGS_TO_REVERSE

Constructor Detail

SAMRecordUtil

Method Detail

reverseComplement

reverseComplement

reverseComplement