# Package org.snpeff.binseq

package org.snpeff.binseq

Related Packages
Package
Description
org.snpeff
org.snpeff.binseq.coder
org.snpeff.binseq.comparator
org.snpeff.binseq.indexer
Classes
Class
Description
BinarySequence
Base class for a binary 'read'.
DnaAndQualitySequence
Binary 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 , ..
DnaAndQualitySequenceWithId
DnaAndQualitySequence with an ID
DnaNSequence
Binary packed DNA sequence that allows also 'N' bases: {A, C, G, T, N}
DnaSequence
Binary 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} invalid input: '<'=> {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)
DnaSequenceByte
Binary packed DNA sequence.
DnaSequenceId
Binary packed DNA sequence with an ID (long)
DnaSequencePe
Pair end DNA sequence (binary packed) It consists of 2 DNA sequences separated by a gap.
GenomicSequences
This class stores all "relevant" sequences in a genome This class is able to: i) Add all regions of interest ii) Store genomic sequences for those regions of interest iii) Retrieve genomic sequences by interval
IdGenerator
Generates Id