Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.filter | |
htsjdk.samtools.util | |
htsjdk.tribble | |
htsjdk.variant.vcf |
Modifier and Type | Interface and Description |
---|---|
interface |
SAMRecordIterator
A general interface that adds functionality to a CloseableIterator of
SAMRecords.
|
Modifier and Type | Class and Description |
---|---|
static class |
CRAMFileReader.IntervalIterator |
class |
CRAMIterator |
class |
DownsamplingIterator
Abstract base class for all DownsamplingIterators that provides a uniform interface for recording
and reporting statistics bout how many records have been kept and discarded.
|
class |
DuplicateSetIterator
An iterator of sets of duplicates.
|
class |
MergingSamRecordIterator
Provides an iterator interface for merging multiple underlying iterators into a single
iterable stream.
|
static class |
SamPairUtil.SetMateInfoIterator
A class to iterate through SAMRecords and set mate information on the given records, and optionally
set the mate cigar tag (true by default).
|
static class |
SamReader.AssertingIterator |
class |
SRAIterator
SRA iterator which returns SAMRecords for requested list of chunks
|
Modifier and Type | Method and Description |
---|---|
CloseableIterator<SAMRecord> |
SRAFileReader.getIterator() |
CloseableIterator<SAMRecord> |
SamReader.PrimitiveSamReader.getIterator() |
CloseableIterator<SAMRecord> |
SRAFileReader.getIterator(SAMFileSpan chunks) |
CloseableIterator<SAMRecord> |
CRAMFileReader.getIterator(SAMFileSpan fileSpan) |
CloseableIterator<SAMRecord> |
SamReader.PrimitiveSamReader.getIterator(SAMFileSpan fileSpan) |
CloseableIterator<SAMRecord> |
SAMRecordSetBuilder.iterator()
Returns a CloseableIterator over the collection of SAMRecords.
|
CloseableIterator<java.util.Map.Entry<KEY,REC>> |
CoordinateSortedPairInfoMap.iterator()
Creates an iterator over all elements in map, in arbitrary order.
|
CloseableIterator<SAMRecord> |
SRAFileReader.query(QueryInterval[] intervals,
boolean contained) |
CloseableIterator<SAMRecord> |
CRAMFileReader.query(QueryInterval[] intervals,
boolean contained) |
CloseableIterator<SAMRecord> |
SamReader.PrimitiveSamReader.query(QueryInterval[] intervals,
boolean contained) |
CloseableIterator<SAMRecord> |
SRAFileReader.queryAlignmentStart(java.lang.String sequence,
int start) |
CloseableIterator<SAMRecord> |
CRAMFileReader.queryAlignmentStart(java.lang.String sequence,
int start) |
CloseableIterator<SAMRecord> |
SamReader.PrimitiveSamReader.queryAlignmentStart(java.lang.String sequence,
int start) |
CloseableIterator<SAMRecord> |
SRAFileReader.queryUnmapped() |
CloseableIterator<SAMRecord> |
CRAMFileReader.queryUnmapped() |
CloseableIterator<SAMRecord> |
SamReader.PrimitiveSamReader.queryUnmapped() |
Constructor and Description |
---|
AssertingIterator(CloseableIterator<SAMRecord> iterator) |
DuplicateSetIterator(CloseableIterator<SAMRecord> iterator,
SAMFileHeader header) |
DuplicateSetIterator(CloseableIterator<SAMRecord> iterator,
SAMFileHeader header,
boolean preSorted)
Allows the user of this iterator to skip the sorting of the input if the input is already sorted.
|
IntervalIterator(CloseableIterator<SAMRecord> delegate,
QueryInterval interval) |
IntervalIterator(CloseableIterator<SAMRecord> delegate,
QueryInterval interval,
boolean overlap) |
NotPrimarySkippingIterator(CloseableIterator<SAMRecord> underlyingIt) |
SecondaryOrSupplementarySkippingIterator(CloseableIterator<SAMRecord> underlyingIt) |
Constructor and Description |
---|
MergingSamRecordIterator(SamFileHeaderMerger headerMerger,
java.util.Map<SamReader,CloseableIterator<SAMRecord>> iterators,
boolean assumeSorted)
Add a set of SAM file iterators to the merging iterator.
|
Modifier and Type | Class and Description |
---|---|
class |
FilteringIterator
Filtering Iterator which takes a filter and an iterator and iterates through only those records
which are not rejected by the filter.
|
Modifier and Type | Class and Description |
---|---|
class |
DelegatingIterator<T>
Simple iterator class that delegates all method calls to an underlying iterator.
|
class |
MergingIterator<T>
An iterator over Iterators that return Ts.
|
class |
PeekableIterator<Object>
Generic Closable Iterator that allows you to peek at the next value before calling next
|
class |
SamLocusIterator
Iterator that traverses a SAM File, accumulating information on a per-locus basis.
|
Modifier and Type | Method and Description |
---|---|
CloseableIterator<T> |
SortingCollection.iterator()
Prepare to iterate through the records in order.
|
CloseableIterator<SAMRecord> |
SamRecordIntervalIteratorFactory.makeSamRecordIntervalIterator(SamReader samReader,
java.util.List<Interval> uniqueIntervals,
boolean useIndex) |
Modifier and Type | Method and Description |
---|---|
long |
QualityEncodingDetector.add(long maxRecords,
CloseableIterator<SAMRecord> iterator) |
long |
QualityEncodingDetector.add(long maxRecords,
CloseableIterator<SAMRecord> iterator,
boolean useOriginalQualities)
Adds the provided iterator's records (optionally using the original qualities) to the detector.
|
static FastqQualityFormat |
QualityEncodingDetector.detect(long maxRecords,
CloseableIterator<SAMRecord> iterator) |
static FastqQualityFormat |
QualityEncodingDetector.detect(long maxRecords,
CloseableIterator<SAMRecord> iterator,
boolean useOriginalQualities)
Reads through the records in the provided SAM reader and uses their quality scores to determine the quality
format used in the SAM.
|
Constructor and Description |
---|
MergingIterator(java.util.Comparator<T> comparator,
java.util.Collection<CloseableIterator<T>> iterators)
Creates a MergingIterator over the given Collection of iterators whose elements will be
returned in the order defined by the given Comparator.
|
Modifier and Type | Interface and Description |
---|---|
interface |
CloseableTribbleIterator<T extends Feature>
The basic iterator we use in Tribble, which allows closing and basic iteration.
|
Modifier and Type | Method and Description |
---|---|
CloseableIterator<VariantContext> |
VCFFileReader.iterator()
Returns an iterator over all records in this VCF/BCF file.
|
CloseableIterator<VariantContext> |
VCFFileReader.query(java.lang.String chrom,
int start,
int end)
Queries for records within the region specified.
|