Uses of Package
org.snpeff.binseq
Packages that use org.snpeff.binseq
Package
Description
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Classes in org.snpeff.binseq used by org.snpeff.binseqClassDescriptionBase class for a binary 'read'.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 , ..DnaAndQualitySequence with an IDBinary packed DNA sequence that allows also 'N' bases: {A, C, G, T, N}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)Binary packed DNA sequence with an ID (long)Pair end DNA sequence (binary packed) It consists of 2 DNA sequences separated by a gap.
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Classes in org.snpeff.binseq used by org.snpeff.binseq.comparatorClassDescriptionBase class for a binary 'read'.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 , ..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)
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Classes in org.snpeff.binseq used by org.snpeff.binseq.indexerClassDescriptionBase class for a binary 'read'.Binary packed DNA sequence with an ID (long)
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Classes in org.snpeff.binseq used by org.snpeff.fileIterator
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Classes in org.snpeff.binseq used by org.snpeff.intervalClassDescriptionBinary 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)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
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Classes in org.snpeff.binseq used by org.snpeff.overlapClassDescriptionBase class for a binary 'read'.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)