Package | Description |
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htsjdk.samtools |
Modifier and Type | Method and Description |
---|---|
QueryInterval |
SAMFileReader.makeQueryInterval(java.lang.String sequence,
int start)
Deprecated.
Convenience method to create a QueryInterval that goes from start to end of given sequence.
|
QueryInterval |
SAMFileReader.makeQueryInterval(java.lang.String sequence,
int start,
int end)
Deprecated.
Convenience method to create a QueryInterval
|
static QueryInterval[] |
QueryInterval.optimizeIntervals(QueryInterval[] inputIntervals) |
Modifier and Type | Method and Description |
---|---|
boolean |
QueryInterval.abuts(QueryInterval other) |
int |
QueryInterval.compareTo(QueryInterval other) |
static QueryInterval[] |
QueryInterval.optimizeIntervals(QueryInterval[] inputIntervals) |
boolean |
QueryInterval.overlaps(QueryInterval other) |
CloseableIterator<SAMRecord> |
CRAMFileReader.query(QueryInterval[] intervals,
boolean contained) |
SAMRecordIterator |
SamReader.query(QueryInterval[] intervals,
boolean contained)
Iterate over records that match one of the given intervals.
|
CloseableIterator<SAMRecord> |
SamReader.PrimitiveSamReader.query(QueryInterval[] intervals,
boolean contained) |
SAMRecordIterator |
SamReader.PrimitiveSamReaderToSamReaderAdapter.query(QueryInterval[] intervals,
boolean contained) |
SAMRecordIterator |
SAMFileReader.query(QueryInterval[] intervals,
boolean contained)
Deprecated.
Iterate over records that match one of the given intervals.
|
CloseableIterator<SAMRecord> |
SRAFileReader.query(QueryInterval[] intervals,
boolean contained) |
SAMRecordIterator |
SamReader.queryContained(QueryInterval[] intervals)
Iterate over records that are contained in the given interval.
|
SAMRecordIterator |
SamReader.PrimitiveSamReaderToSamReaderAdapter.queryContained(QueryInterval[] intervals) |
SAMRecordIterator |
SAMFileReader.queryContained(QueryInterval[] intervals)
Deprecated.
Iterate over records that are contained in the given interval.
|
SAMRecordIterator |
SamReader.queryOverlapping(QueryInterval[] intervals)
Iterate over records that overlap any of the given intervals.
|
SAMRecordIterator |
SamReader.PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(QueryInterval[] intervals) |
SAMRecordIterator |
SAMFileReader.queryOverlapping(QueryInterval[] intervals)
Deprecated.
Iterate over records that overlap any of the given intervals.
|
Constructor and Description |
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IntervalIterator(CloseableIterator<SAMRecord> delegate,
QueryInterval interval) |
IntervalIterator(CloseableIterator<SAMRecord> delegate,
QueryInterval interval,
boolean overlap) |