Package org.snpeff.binseq


package org.snpeff.binseq
  • Classes
    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} 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)
    Binary packed DNA sequence.
    Binary packed DNA sequence with an ID (long)
    Pair end DNA sequence (binary packed) It consists of 2 DNA sequences separated by a gap.
    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
    Generates Id