Package | Description |
---|---|
htsjdk.samtools.filter | |
htsjdk.samtools.liftover | |
htsjdk.samtools.util |
Constructor and Description |
---|
IntervalFilter(java.util.List<Interval> intervals,
SAMFileHeader samHeader)
Prepare to filter out SAMRecords that do not overlap the given list of intervals
|
Modifier and Type | Method and Description |
---|---|
Interval |
LiftOver.liftOver(Interval interval)
Lift over the given interval to the new genome build using the liftOverMinMatch set for this
LiftOver object.
|
Interval |
LiftOver.liftOver(Interval interval,
double liftOverMinMatch)
Lift over the given interval to the new genome build.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<LiftOver.PartialLiftover> |
LiftOver.diagnosticLiftover(Interval interval) |
Interval |
LiftOver.liftOver(Interval interval)
Lift over the given interval to the new genome build using the liftOverMinMatch set for this
LiftOver object.
|
Interval |
LiftOver.liftOver(Interval interval,
double liftOverMinMatch)
Lift over the given interval to the new genome build.
|
Modifier and Type | Method and Description |
---|---|
Interval |
Interval.clone() |
Interval |
Interval.intersect(Interval that)
Returns a new Interval that represents the intersection between the two intervals.
|
Interval |
Interval.pad(int left,
int right)
Returns a new interval that is padded by the amount of bases specified on either side.
|
Modifier and Type | Method and Description |
---|---|
static java.util.List<Interval> |
IntervalList.breakIntervalsAtBandMultiples(java.util.List<Interval> intervals,
int bandMultiple)
Given a list of Intervals and a band multiple, this method will return a list of Intervals such that all of the intervals
do not straddle integer multiples of that band.
|
java.util.Set<java.util.Map.Entry<Interval,T>> |
IntervalTreeMap.entrySet() |
java.util.List<Interval> |
IntervalList.getIntervals()
Gets the set of intervals as held internally.
|
java.util.List<Interval> |
IntervalList.getUniqueIntervals()
Deprecated.
|
java.util.List<Interval> |
IntervalList.getUniqueIntervals(boolean concatenateNames)
Deprecated.
|
static java.util.List<Interval> |
IntervalList.getUniqueIntervals(IntervalList list,
boolean concatenateNames)
Merges list of intervals and reduces them like htsjdk.samtools.util.IntervalList#getUniqueIntervals()
|
static java.util.List<Interval> |
IntervalList.getUniqueIntervals(IntervalList list,
boolean concatenateNames,
boolean enforceSameStrands)
Merges list of intervals and reduces them like htsjdk.samtools.util.IntervalList#getUniqueIntervals()
|
java.util.Iterator<Interval> |
IntervalList.iterator()
Returns an iterator over the intervals.
|
Modifier and Type | Method and Description |
---|---|
boolean |
Interval.abuts(Interval other)
Returns true if this interval overlaps the other interval, otherwise false.
|
void |
IntervalList.add(Interval interval)
Adds an interval to the list of intervals.
|
void |
OverlapDetector.addLhs(T object,
Interval interval)
Adds a mapping to the set of mappings against which to match candidates.
|
int |
Interval.compareTo(Interval that)
Sort based on sequence.compareTo, then start pos, then end pos
with null objects coming lexically last
|
static boolean |
IntervalUtil.contains(Interval interval,
java.lang.String sequenceName,
long position)
Return true if the sequence/position lie in the provided interval.
|
boolean |
IntervalTreeMap.containsContained(Interval key)
Test if this contains an object that is contained by 'key'
|
boolean |
IntervalTreeMap.containsKey(Interval key) |
boolean |
IntervalTreeMap.containsOverlapping(Interval key)
Test overlapping interval
|
T |
IntervalTreeMap.get(Interval key) |
java.util.Collection<T> |
IntervalTreeMap.getContained(Interval key) |
int |
Interval.getIntersectionLength(Interval other) |
java.util.Collection<T> |
IntervalTreeMap.getOverlapping(Interval key) |
java.util.Collection<T> |
OverlapDetector.getOverlaps(Interval rhs)
Gets the collection of objects that overlap the provided mapping.
|
Interval |
Interval.intersect(Interval that)
Returns a new Interval that represents the intersection between the two intervals.
|
boolean |
Interval.intersects(Interval other)
Returns true if this interval overlaps the other interval, otherwise false.
|
T |
IntervalTreeMap.put(Interval key,
T value) |
T |
IntervalTreeMap.remove(Interval key) |
Modifier and Type | Method and Description |
---|---|
void |
IntervalList.addall(java.util.Collection<Interval> intervals)
Adds a Collection of intervals to the list of intervals.
|
void |
OverlapDetector.addAll(java.util.List<T> objects,
java.util.List<Interval> intervals)
Adds all items to the overlap detector.
|
static void |
IntervalUtil.assertOrderedNonOverlapping(java.util.Iterator<Interval> intervals,
SAMSequenceDictionary sequenceDictionary)
Throws RuntimeException if the given intervals are not locus ordered and non-overlapping
|
static java.util.List<Interval> |
IntervalList.breakIntervalsAtBandMultiples(java.util.List<Interval> intervals,
int bandMultiple)
Given a list of Intervals and a band multiple, this method will return a list of Intervals such that all of the intervals
do not straddle integer multiples of that band.
|
static long |
Interval.countBases(java.util.Collection<Interval> intervals)
Counts the total number of bases a collection of intervals.
|
CloseableIterator<SAMRecord> |
SamRecordIntervalIteratorFactory.makeSamRecordIntervalIterator(SamReader samReader,
java.util.List<Interval> uniqueIntervals,
boolean useIndex) |
Constructor and Description |
---|
IntervalTreeMap(java.util.Map<? extends Interval,? extends T> map) |