Uses of Package
org.snpeff.binseq

Packages that use org.snpeff.binseq
  • Class
    Description
    Base 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 ID
    Binary 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.
  • Class
    Description
    Base 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)
  • Class
    Description
    Base class for a binary 'read'.
    Binary packed DNA sequence with an ID (long)
  • Class
    Description
    Base class for a binary 'read'.
  • Class
    Description
    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)
    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
  • Class
    Description
    Base 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)