# Uses of Package
org.snpeff.binseq

Packages that use org.snpeff.binseq
Package
Description
org.snpeff.binseq
org.snpeff.binseq.comparator
org.snpeff.binseq.indexer
org.snpeff.fileIterator
org.snpeff.interval
org.snpeff.overlap

Classes in org.snpeff.binseq used by org.snpeff.binseq
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)
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.
Classes in org.snpeff.binseq used by org.snpeff.binseq.comparator
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 , ..
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)
Classes in org.snpeff.binseq used by org.snpeff.binseq.indexer
Class
Description
BinarySequence
Base class for a binary 'read'.
DnaSequenceId
Binary packed DNA sequence with an ID (long)
Classes in org.snpeff.binseq used by org.snpeff.fileIterator
Class
Description
BinarySequence
Base class for a binary 'read'.
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)
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.
Classes in org.snpeff.binseq used by org.snpeff.interval
Class
Description
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)
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
Classes in org.snpeff.binseq used by org.snpeff.overlap
Class
Description
BinarySequence
Base class for a binary 'read'.
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)