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// Author: David Alexander
#pragma once
namespace ConsensusCore {
//
// Scoring params for Needleman-Wunsch or Smith-Waterman style aligners
//
struct AlignParams
{
int Match;
int Mismatch;
int Insert;
int Delete;
AlignParams(int match, int mismatch, int insert, int delete_);
// Edit distance params
static AlignParams Default();
};
enum AlignMode
{
GLOBAL = 0, // Global in both sequences
SEMIGLOBAL = 1, // Global in query, local in target
LOCAL = 2 // Local in both sequences
};
struct AlignConfig
{
AlignParams Params;
AlignMode Mode;
AlignConfig(AlignParams params, AlignMode mode);
// Default corresponds to global alignment mode, edit distance params
static AlignConfig Default();
};
}
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