org.bdgenomics.adam.algorithms.smithwaterman
CIGAR strings and alignment start positions from the pairwise alignment process.
CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".
CIGAR strings and alignment start positions from the pairwise alignment process.
CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".
CIGAR strings and alignment start positions from the pairwise alignment process.
CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".
CIGAR strings and alignment start positions from the pairwise alignment process.
CIGAR strings and alignment start positions from the pairwise alignment process. The alignment start position may be non-zero if two strings are the same length, but the highest scoring alignment has bases deleted in one string/inserted in the other. In this case, some bases at the start/end of one string are expected to be "trimmed".
Abstract class for implementing a Smith-Waterman pairwise alignment.
Contains shell code for everything except for building the pairwise alignment score matrix. This way, a new scoring method (e.g., affine gap, residue specific scores) can be implemented without needing to implement core functionality like trackback, etc.