sam.h

/* 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 "nw.h"
#include "qseqs.h"

char * makeCigar(Qseqs *Cigar, const Aln *aligned);
void saminit(Qseqs *template_name, FILE *name_file, int *template_lengths, int DB_size, char *cmd);
int samwrite(const Qseqs *qseq, const Qseqs *header, const Qseqs *Qual, char *rname, const Aln *aligned, const int *stats);