/* Philip T.L.C. Clausen Jan 2017 plan@dtu.dk */

/*
 * Copyright (c) 2017, Philip Clausen, Technical University of Denmark
 * All rights reserved.
 * 
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 * 
 *		http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
*/
#define _XOPEN_SOURCE 600
#include "chain.h"
#include "compdna.h"
#include "hashmapindex.h"
#include "nw.h"

AlnScore KMA(const HashMap_index *template_index, const unsigned char *qseq, int q_len, Aln *aligned, Aln *Frag_align, int min, int max, int mq, double scoreT, AlnPoints *points, NWmat *matrices);
AlnScore KMA_score(const HashMap_index *template_index, const unsigned char *qseq, int q_len, const CompDNA *qseq_comp, int mq, double scoreT, AlnPoints *points, NWmat *matrices);
int preseed(const HashMap_index *template_index, unsigned char *qseq, int q_len);
void intcpy(int *dest, int *src, int size);
int anker_rc(const HashMap_index *template_index, unsigned char *qseq, int q_len, AlnPoints *points);