Package org.snpeff.overlap
package org.snpeff.overlap
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ClassesClassDescriptionCounts how many bases changed, given an XOR between two longsOverlap<S extends BinarySequence>Calculates the best overlap between two sequences Note: An overlap is a simple 'alignment' which can only contain gaps at the beginning or at the end of the sequences.Rotates a binary packed sequence WARNING: We only rotate up to Coder.basesPerWord() because after that the sequences are the same (with an integer offset) NOTE: Left rotation 'n' is the same as a right rotation 'Coder.basesPerWord() - n'