org.bdgenomics.adam.algorithms

# smithwaterman

#### package smithwaterman

Visibility

1. Public
2. All

### Type Members

1. #### trait SmithWaterman extends Serializable

   Abstract class for implementing a Smith-Waterman pairwise alignment.

   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.

2. #### case class SmithWatermanConstantGapScoring (xSequence: String, ySequence: String, wMatch: Double, wMismatch: Double, wInsert: Double, wDelete: Double) extends SmithWatermanGapScoringFromFn with Product with Serializable

   Performs a pairwise alignment of two sequences using constant penalties.

   Performs a pairwise alignment of two sequences using constant penalties.

   xSequence

     The first sequence in the pair.

   ySequence

     The second sequence in the pair.

   wMatch

     The alignment gap penalty for a residue match.

   wMismatch

     The alignment gap penalty for a residue mismatch.

   wInsert

     The alignment gap penalty for an insertion in the first sequence.

   wDelete

     The alignment gap penalty for a deletion in the first sequence.

   See also

     scoreFn

### Ungrouped