| Interface | Description |
|---|---|
| SingleSequenceReferenceAligner.TriFunction<T,U,V,W> | |
| SVIntervalTree.Entry<V1> |
| Class | Description |
|---|---|
| CNVInputReader | |
| ComplexityPartitioner |
A Spark Partitioner that puts tasks with greater complexities into earlier partitions.
|
| ExtractOriginalAlignmentRecordsByNameSpark |
Subsets reads by name
|
| GATKSVVCFConstants | |
| GATKSVVCFHeaderLines | |
| KmerAndCount |
A
|
| KmerAndCount.Serializer | |
| PairedStrandedIntervals | |
| PairedStrandedIntervalTree<V> | |
| PairedStrandedIntervalTree.Serializer<T> | |
| SingleSequenceReferenceAligner<T,U> |
Encompasses an aligner to a single-sequence reference.
|
| Strand.Serializer | |
| StrandedInterval |
Represents an interval and strand from the reference genome.
|
| StrandedInterval.Serializer | |
| SvCigarUtils |
Various utility functions helping calling structural variants.
|
| SVContext |
Variant context with additional method to mine the structural variant specific information from structural
variant records.
|
| SVDUSTFilteredKmerizer |
An iterator over kmers with a specified maximum DUST-style, low-complexity score.
|
| SVFastqUtils |
Memory-economical utilities for producing a FASTQ file.
|
| SVFastqUtils.FastqRead | |
| SVFastqUtils.FastqRead.Serializer | |
| SVFastqUtils.Mapping | |
| SVFileUtils | |
| SVInterval |
Naturally collating, simple interval.
|
| SVInterval.Serializer | |
| SVIntervalTree<V> |
A Red-Black tree with intervals for keys.
|
| SVIntervalTree.Serializer<T> | |
| SVIntervalTree.ValuesIterator<V1> | |
| SVKmer | |
| SVKmerizer |
Iterator over successive Kmers from a sequence of characters.
|
| SVKmerizer.ASCIICharSequence | |
| SVKmerLong |
An immutable SVKmerLong.
|
| SVKmerLong.Serializer | |
| SVKmerShort |
An immutable SVKmerShort.
|
| SVKmerShort.Serializer | |
| SVLocation | |
| SVReferenceUtils | |
| SVUtils |
Useful scraps of this and that.
|
| SVUtils.IteratorFilter<T> | |
| SVVCFReader | |
| SVVCFWriter |
A utility class that writes out variants to a VCF file.
|
| TextMDCodec | |
| TextMDCodec.DeletionMDElement | |
| TextMDCodec.MatchMDElement | |
| TextMDCodec.MDElement | |
| TextMDCodec.MismatchMDElement |
| Enum | Description |
|---|---|
| Strand | |
| SVKmer.Base |