Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.util |
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
|
Modifier and Type | Method and Description |
---|---|
java.util.List<CigarElement> |
Cigar.getCigarElements() |
java.util.Iterator<CigarElement> |
Cigar.iterator()
shortcut to
getCigarElements().iterator() |
Modifier and Type | Method and Description |
---|---|
void |
Cigar.add(CigarElement cigarElement) |
Modifier and Type | Method and Description |
---|---|
static int |
Cigar.getReadLength(java.util.List<CigarElement> cigarElements) |
Constructor and Description |
---|
Cigar(java.util.List<CigarElement> cigarElements) |
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.
|
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.
|