Package | Description |
---|---|
htsjdk.samtools |
Modifier and Type | Class and Description |
---|---|
static class |
CRAMFileReader.IntervalIterator |
class |
CRAMIterator |
static class |
SamReader.AssertingIterator |
class |
SRAIterator
SRA iterator which returns SAMRecords for requested list of chunks
|
Modifier and Type | Method and Description |
---|---|
SAMRecordIterator |
CRAMFileReader.IntervalIterator.assertSorted(SAMFileHeader.SortOrder sortOrder) |
SAMRecordIterator |
SamReader.AssertingIterator.assertSorted(SAMFileHeader.SortOrder sortOrder) |
SAMRecordIterator |
SRAIterator.assertSorted(SAMFileHeader.SortOrder sortOrder) |
SAMRecordIterator |
CRAMIterator.assertSorted(SAMFileHeader.SortOrder sortOrder) |
SAMRecordIterator |
SAMRecordIterator.assertSorted(SAMFileHeader.SortOrder sortOrder)
Establishes that records returned by this iterator are expected to
be in the specified sort order.
|
SAMRecordIterator |
CRAMFileReader.getIterator() |
SAMRecordIterator |
SAMFileReader.iterator()
Deprecated.
Iterate through file in order.
|
SAMRecordIterator |
SAMFileTruncatedReader.iterator()
Deprecated.
|
SAMRecordIterator |
SamReader.iterator()
Iterate through file in order.
|
SAMRecordIterator |
SamReader.PrimitiveSamReaderToSamReaderAdapter.iterator() |
SAMRecordIterator |
SAMFileReader.iterator(SAMFileSpan chunks)
Deprecated.
Iterate through the given chunks in the file.
|
SAMRecordIterator |
SRAFileReader.iterator(SAMFileSpan chunks)
Iterate through the given chunks in the file.
|
SAMRecordIterator |
CRAMFileReader.iterator(SAMFileSpan fileSpan) |
SAMRecordIterator |
SAMFileTruncatedReader.iterator(SAMFileSpan chunks)
Deprecated.
|
SAMRecordIterator |
SamReader.Indexing.iterator(SAMFileSpan chunks)
Iterate through the given chunks in the file.
|
SAMRecordIterator |
SamReader.PrimitiveSamReaderToSamReaderAdapter.iterator(SAMFileSpan chunks) |
SAMRecordIterator |
SAMFileReader.query(QueryInterval[] intervals,
boolean contained)
Deprecated.
Iterate over records that match one of the given intervals.
|
SAMRecordIterator |
SamReader.query(QueryInterval[] intervals,
boolean contained)
Iterate over records that match one of the given intervals.
|
SAMRecordIterator |
SamReader.PrimitiveSamReaderToSamReaderAdapter.query(QueryInterval[] intervals,
boolean contained) |
SAMRecordIterator |
SAMFileReader.query(java.lang.String sequence,
int start,
int end,
boolean contained)
Deprecated.
Iterate over records that match the given interval.
|
SAMRecordIterator |
SamReader.query(java.lang.String sequence,
int start,
int end,
boolean contained)
Iterate over records that match the given interval.
|
SAMRecordIterator |
SamReader.PrimitiveSamReaderToSamReaderAdapter.query(java.lang.String sequence,
int start,
int end,
boolean contained) |
SAMRecordIterator |
SAMFileReader.queryAlignmentStart(java.lang.String sequence,
int start)
Deprecated.
Iterate over records that map to the given sequence and start at the given position.
|
SAMRecordIterator |
SamReader.queryAlignmentStart(java.lang.String sequence,
int start)
Iterate over records that map to the given sequence and start at the given position.
|
SAMRecordIterator |
SamReader.PrimitiveSamReaderToSamReaderAdapter.queryAlignmentStart(java.lang.String sequence,
int start) |
SAMRecordIterator |
SAMFileReader.queryContained(QueryInterval[] intervals)
Deprecated.
Iterate over records that are contained in the given interval.
|
SAMRecordIterator |
SamReader.queryContained(QueryInterval[] intervals)
Iterate over records that are contained in the given interval.
|
SAMRecordIterator |
SamReader.PrimitiveSamReaderToSamReaderAdapter.queryContained(QueryInterval[] intervals) |
SAMRecordIterator |
SAMFileReader.queryContained(java.lang.String sequence,
int start,
int end)
Deprecated.
Iterate over records that are contained in the given interval.
|
SAMRecordIterator |
SamReader.queryContained(java.lang.String sequence,
int start,
int end)
Iterate over records that are contained in the given interval.
|
SAMRecordIterator |
SamReader.PrimitiveSamReaderToSamReaderAdapter.queryContained(java.lang.String sequence,
int start,
int end) |
SAMRecordIterator |
SAMFileReader.queryOverlapping(QueryInterval[] intervals)
Deprecated.
Iterate over records that overlap any of the given intervals.
|
SAMRecordIterator |
SamReader.queryOverlapping(QueryInterval[] intervals)
Iterate over records that overlap any of the given intervals.
|
SAMRecordIterator |
SamReader.PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(QueryInterval[] intervals) |
SAMRecordIterator |
SAMFileReader.queryOverlapping(java.lang.String sequence,
int start,
int end)
Deprecated.
Iterate over records that overlap the given interval.
|
SAMRecordIterator |
SamReader.queryOverlapping(java.lang.String sequence,
int start,
int end)
Iterate over records that overlap the given interval.
|
SAMRecordIterator |
SamReader.PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(java.lang.String sequence,
int start,
int end) |
SAMRecordIterator |
SAMFileReader.queryUnmapped()
Deprecated.
|
SAMRecordIterator |
SamReader.queryUnmapped() |
SAMRecordIterator |
SamReader.PrimitiveSamReaderToSamReaderAdapter.queryUnmapped() |