Uses of Package
org.snpeff.binseq
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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 IDDnaNSequence 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} <=> {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} <=> {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'. -
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} <=> {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} <=> {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)