org.bdgenomics.adam.algorithms.smithwaterman
SmithWatermanConstantGapScoring
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package smithwaterman
org.bdgenomics.adam.algorithms.smithwaterman
The first sequence in the pair.
The second sequence in the pair.
The alignment gap penalty for a residue match.
The alignment gap penalty for a residue mismatch.
The alignment gap penalty for an insertion in the first sequence.
The alignment gap penalty for a deletion in the first sequence.
Builds Smith-Waterman score matrix by calling scoring function for all residue pairs.
Builds Smith-Waterman score matrix by calling scoring function for all residue pairs.
2D array of doubles, along with move direction at each point.
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".
Scores residues using scoring constants.
Scores residues using scoring constants.
* If a deletion is observed (xResidue is a gap), then the deletion penalty is returned. * If an insertion is observed (yResidue is a gap), then the insertion penalty is returned. * Else, the residues are compared, and either the match or mismatch penalty is returned.
The position indices are ignored, so no affine/open-continue gap model is incorporated.
Residue position from first sequence.
Residue position from second sequence.
Residue from first sequence.
Residue from second sequence.
Returns the gap score for this residue pair.
The alignment gap penalty for a deletion in the first sequence.
The alignment gap penalty for an insertion in the first sequence.
The alignment gap penalty for a residue match.
The alignment gap penalty for a residue mismatch.
The first sequence in the pair.
The first sequence in the pair.
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".
The second sequence in the pair.
The second sequence in the pair.
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".
Performs a pairwise alignment of two sequences using constant penalties.
The first sequence in the pair.
The second sequence in the pair.
The alignment gap penalty for a residue match.
The alignment gap penalty for a residue mismatch.
The alignment gap penalty for an insertion in the first sequence.
The alignment gap penalty for a deletion in the first sequence.
scoreFn