qseqs.c

/* 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 <stdlib.h>
#include "pherror.h"
#include "qseqs.h"

Qseqs * setQseqs(int size) {
	
	Qseqs *dest;
	
	dest = smalloc(sizeof(Qseqs));
	dest->len = 0;
	dest->size = size;
	dest->seq = smalloc(size);
	
	return dest;
}

void destroyQseqs(Qseqs *dest) {
	free(dest->seq);
	free(dest);
}

void insertKmerBound(Qseqs *header, int start, int end) {
	
	int *seq;
	
	if((header->len + 2 * sizeof(int)) < header->size) {
		header->size = (header->len + 2 * sizeof(int)) << 1;
		if(!(header->seq = realloc(header->seq, header->size))) {
			ERROR();
		}
	}
	header->seq[header->len] = 0;
	seq = (int *) (header->seq + header->len + 1);
	*seq = start;
	*++seq = end;
	header->len += (2 * sizeof(int) + 1);
	
}

void rcQseqs(Qseqs *qseq) {
	
	int i;
	unsigned char nuc, *seq, *rseq, bases[] = {3, 2, 1, 0};
	
	seq = qseq->seq;
	rseq = seq + qseq->len - 1;
	i = qseq->len / 2 + 1;
	while(--i) {
		nuc = bases[*seq];
		*seq = bases[*rseq];
		*rseq = nuc;
		--rseq;
		++seq;
	}
	if(qseq->len & 1) {
		*seq = bases[*seq];
	}
}