Uses of Class
htsjdk.samtools.CigarElement

Packages that use CigarElement

Package	Description
htsjdk.samtools
htsjdk.samtools.util

Uses of CigarElement in htsjdk.samtools

Methods in htsjdk.samtools that return CigarElement

Modifier and Type	Method and Description
CigarElement	Cigar.getCigarElement(int i)
CigarElement	Cigar.getFirstCigarElement() returns the first cigar element
CigarElement	Cigar.getLastCigarElement() returns the last cigar element

Methods in htsjdk.samtools that return types with arguments of type CigarElement

Modifier and Type	Method and Description
java.util.List<CigarElement>	Cigar.getCigarElements()
java.util.Iterator<CigarElement>	Cigar.iterator() shortcut to getCigarElements().iterator()

Methods in htsjdk.samtools with parameters of type CigarElement

Modifier and Type	Method and Description
void	Cigar.add(CigarElement cigarElement)

Method parameters in htsjdk.samtools with type arguments of type CigarElement

Modifier and Type	Method and Description
static int	Cigar.getReadLength(java.util.List<CigarElement> cigarElements)

Constructor parameters in htsjdk.samtools with type arguments of type CigarElement

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

Uses of CigarElement in htsjdk.samtools.util

Methods in htsjdk.samtools.util that return types with arguments of type CigarElement

Modifier and Type	Method and Description
static java.util.List<CigarElement>	CigarUtil.softClipEndOfRead(int clipFrom, java.util.List<CigarElement> oldCigar) adjust the cigar based on adapter clipping.

Method parameters in htsjdk.samtools.util with type arguments of type CigarElement

Modifier and Type	Method and Description
static char[]	CigarUtil.cigarArrayFromElements(java.util.List<CigarElement> cigar)
static java.util.List<CigarElement>	CigarUtil.softClipEndOfRead(int clipFrom, java.util.List<CigarElement> oldCigar) adjust the cigar based on adapter clipping.