Uses of Class
org.snpeff.binseq.BinarySequence
Packages that use BinarySequence
Package
Description
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Uses of BinarySequence in org.snpeff.binseq
Subclasses of BinarySequence in org.snpeff.binseqModifier and TypeClassDescriptionclassBinary packed DNA sequence and base calling quality Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 8 bits: - Six bits for the base quality [0 , ..classDnaAndQualitySequence with an IDclassBinary packed DNA sequence that allows also 'N' bases: {A, C, G, T, N}classBinary packed DNA sequence Notes: - This is designed for short sequences (such as "short reads") - Every base is encoded in 2 bits {a, c, g, t} <=> {0, 1, 2, 3} - All bits are stored in an array of 'words' (integers) - Most significant bits are the first bases in the sequence (makes comparison easier)classBinary packed DNA sequence with an ID (long)classPair end DNA sequence (binary packed) It consists of 2 DNA sequences separated by a gap.Methods in org.snpeff.binseq that return BinarySequenceModifier and TypeMethodDescriptionBinarySequence.clone()BinarySequence.overlap(BinarySequence sequence, int start) Creates a new sequence by overlapping 'this' and 'sequence' E.g.DnaSequence.overlap(BinarySequence sequence, int start) Creates a new sequence by overlapping 'this' and 'sequence' E.g.abstract BinarySequenceBinarySequence.read(DataInputStream dataInStream) Read a sequence from a data streamDnaNSequence.read(DataInputStream dataInStream) Read data in binary formatDnaSequence.read(DataInputStream dataInStream) Read data in binary formatDnaSequenceId.read(DataInputStream dataInStream) Read data in binary formatabstract BinarySequenceBinarySequence.reverseWc()Reverse Watson-Cricks complementDnaNSequence.reverseWc()DnaSequence.reverseWc()DnaSequencePe.reverseWc()Methods in org.snpeff.binseq with parameters of type BinarySequenceModifier and TypeMethodDescriptionintDnaAndQualitySequence.compareTo(BinarySequence o) intDnaSequence.compareTo(BinarySequence o) intDnaSequencePe.compareTo(BinarySequence o) BinarySequence.overlap(BinarySequence sequence, int start) Creates a new sequence by overlapping 'this' and 'sequence' E.g.DnaAndQualitySequence.overlap(BinarySequence sequence, int start) Creates a new sequence by overlapping 'this' and 'sequence' E.g.DnaSequence.overlap(BinarySequence sequence, int start) Creates a new sequence by overlapping 'this' and 'sequence' E.g. -
Uses of BinarySequence in org.snpeff.binseq.comparator
Classes in org.snpeff.binseq.comparator with type parameters of type BinarySequenceModifier and TypeClassDescriptionclassSubsequenceComparator<T extends BinarySequence>Compare two subsequences (actually it compares two sequences from different starting points) -
Uses of BinarySequence in org.snpeff.binseq.indexer
Classes in org.snpeff.binseq.indexer with type parameters of type BinarySequenceModifier and TypeInterfaceDescriptioninterfaceOverlapFilter<T extends BinarySequence>Indicate whether an overlap between two sequences should be considered or notclassOverlapRessult<T extends BinarySequence>An object used to store overlap parametersclassSequenceIndexer<T extends BinarySequence>A collection of sequences that are indexed using some algorithm Note: The ID is just the position in the array.classSuffixIndexerNmer<T extends BinarySequence>Index all suffixes of all the sequences (it indexes using Nmers).Fields in org.snpeff.binseq.indexer declared as BinarySequence -
Uses of BinarySequence in org.snpeff.fileIterator
Classes in org.snpeff.fileIterator with type parameters of type BinarySequenceModifier and TypeClassDescriptionclassBinSeqFileIterator<T extends BinarySequence>Reads all sequences from a file Warning: You should always call "close()" at the end of the iteration. -
Uses of BinarySequence in org.snpeff.overlap
Classes in org.snpeff.overlap with type parameters of type BinarySequenceModifier and TypeClassDescriptionclassOverlap<S extends BinarySequence>Calculates the best overlap between two sequences Note: An overlap is a simple 'alignment' which can only contain gaps at the beginning or at the end of the sequences.