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/* 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.
*/
#include <stdio.h>
#include "filebuff.h"
#include "qseqs.h"
#ifndef FRAG
typedef struct frag Frag;
struct frag {
int buffer[7];
unsigned char *qseq;
unsigned char *header;
struct frag *next;
};
#define FRAG 1
#endif
FILE * printFrags(Frag **alignFrags, int DB_size);
void updateAllFrag(unsigned char *qseq, int q_len, int bestHits, int best_read_score, int *best_start_pos, int *best_end_pos, int *bestTemplates, Qseqs *header, FileBuff *dest);
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