Cigar (htsjdk 2.8.1 API)

java.lang.Object
- htsjdk.samtools.Cigar

All Implemented Interfaces:

java.io.Serializable, java.lang.Iterable<CigarElement>
```
public class Cigar
extends java.lang.Object
implements java.io.Serializable, java.lang.Iterable<CigarElement>
```
A list of CigarElements, which describes how a read aligns with the reference. E.g. the Cigar string 10M1D25M means * match or mismatch for 10 bases * deletion of 1 base * match or mismatch for 25 bases c.f. http://samtools.sourceforge.net/SAM1.pdf for complete CIGAR specification.

See Also:

Serialized Form

Field Summary

Fields
Modifier and Type Field and Description

static long serialVersionUID

Fields
Modifier and Type	Field and Description
`static long`	`serialVersionUID`

Constructor Summary

Constructors
Constructor and Description

Cigar()

Cigar(java.util.List<CigarElement> cigarElements)

Constructors
Constructor and Description
`Cigar()`
`Cigar(java.util.List<CigarElement> cigarElements)`

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`add(CigarElement cigarElement)`
`boolean`	`containsOperator(CigarOperator operator)` returns true if the cigar string contains the given operator
`boolean`	`equals(java.lang.Object o)`
`static Cigar`	`fromCigarOperators(java.util.List<CigarOperator> cigarOperators)` build a new Cigar object from a list of cigar operators.
`CigarElement`	`getCigarElement(int i)`
`java.util.List<CigarElement>`	`getCigarElements()`
`CigarElement`	`getFirstCigarElement()` returns the first cigar element
`CigarElement`	`getLastCigarElement()` returns the last cigar element
`int`	`getPaddedReferenceLength()`
`int`	`getReadLength()`
`static int`	`getReadLength(java.util.List<CigarElement> cigarElements)`
`int`	`getReferenceLength()`
`int`	`hashCode()`
`boolean`	`isClipped()` returns true if the cigar is clipped
`boolean`	`isEmpty()`
`boolean`	`isLeftClipped()` returns true if the cigar string starts With a clipping operator
`boolean`	`isRightClipped()` returns true if the cigar string ends With a clipping operator
`java.util.List<SAMValidationError>`	`isValid(java.lang.String readName, long recordNumber)` Exhaustive validation of CIGAR.
`java.util.Iterator<CigarElement>`	`iterator()` shortcut to `getCigarElements().iterator()`
`int`	`numCigarElements()`
`java.lang.String`	`toString()`

Methods inherited from class java.lang.Object
clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.lang.Iterable
forEach, spliterator

- Field Detail
  - serialVersionUID
```
public static final long serialVersionUID
```
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Cigar
```
public Cigar()
```
  - Cigar
```
public Cigar(java.util.List<CigarElement> cigarElements)
```
- Method Detail
  - getCigarElements
```
public java.util.List<CigarElement> getCigarElements()
```
  - getCigarElement
```
public CigarElement getCigarElement(int i)
```
  - add
```
public void add(CigarElement cigarElement)
```
  - numCigarElements
```
public int numCigarElements()
```
  - isEmpty
```
public boolean isEmpty()
```
  - getReferenceLength
```
public int getReferenceLength()
```
    Returns:
    
    The number of reference bases that the read covers, excluding padding.
  - getPaddedReferenceLength
```
public int getPaddedReferenceLength()
```
    Returns:
    
    The number of reference bases that the read covers, including padding.
  - getReadLength
```
public int getReadLength()
```
    Returns:
    
    The number of read bases that the read covers.
  - getReadLength
```
public static int getReadLength(java.util.List<CigarElement> cigarElements)
```
    Returns:
    
    The number of read bases that the read covers.
  - isValid
```
public java.util.List<SAMValidationError> isValid(java.lang.String readName,
                                                  long recordNumber)
```
    Exhaustive validation of CIGAR. Note that this method deliberately returns null rather than Collections.emptyList() if there are no validation errors, because callers tend to assume that if a non-null list is returned, it is modifiable.
    
    Parameters:
    
    readName - For error reporting only. May be null if not known.
    
    recordNumber - For error reporting only. May be -1 if not known.
    
    Returns:
    
    List of validation errors, or null if no errors.
  - equals
```
public boolean equals(java.lang.Object o)
```
    Overrides:
    
    equals in class java.lang.Object
  - fromCigarOperators
```
public static Cigar fromCigarOperators(java.util.List<CigarOperator> cigarOperators)
```
    build a new Cigar object from a list of cigar operators. This can be used if you have the operators associated to each base in the read. e.g: read length =10 with cigar= [M,M,M,M,M,M,M,M,M,M], here fromCigarOperators would generate the cigar '10M' later the user resolved the 'M' to '=' or 'X', the array is now [=,=,=,=,=,X,X,=,=,=] fromCigarOperators would generate the cigar '5M2X3M'
  - iterator
```
public java.util.Iterator<CigarElement> iterator()
```
    shortcut to getCigarElements().iterator()
    
    Specified by:
    
    iterator in interface java.lang.Iterable<CigarElement>
  - containsOperator
```
public boolean containsOperator(CigarOperator operator)
```
    returns true if the cigar string contains the given operator
  - getFirstCigarElement
```
public CigarElement getFirstCigarElement()
```
    returns the first cigar element
  - getLastCigarElement
```
public CigarElement getLastCigarElement()
```
    returns the last cigar element
  - isLeftClipped
```
public boolean isLeftClipped()
```
    returns true if the cigar string starts With a clipping operator
  - isRightClipped
```
public boolean isRightClipped()
```
    returns true if the cigar string ends With a clipping operator
  - isClipped
```
public boolean isClipped()
```
    returns true if the cigar is clipped
  - hashCode
```
public int hashCode()
```
    Overrides:
    
    hashCode in class java.lang.Object
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object

Class Cigar

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Methods inherited from interface java.lang.Iterable

Field Detail

serialVersionUID

Constructor Detail

Cigar

Cigar

Method Detail

getCigarElements

getCigarElement

add

numCigarElements

isEmpty

getReferenceLength

getPaddedReferenceLength

getReadLength

getReadLength

isValid

equals

fromCigarOperators

iterator

containsOperator

getFirstCigarElement

getLastCigarElement

isLeftClipped

isRightClipped

isClipped

hashCode

toString