/* reverseComplement.c
   Program reading a FASTA file as input (one or multiple sequence)
   and then returning the reverse complementary sequence in the output file.
   It is important to note that for multiple sequence file the first input
   sequence is the last one at the output file and the last one in the input
   is the first one in the output.
   oscart@uma.es
 */

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <ctype.h>
#include <inttypes.h>
#include "commonFunctions.h"

#define SEQSIZE 2000000000
#define READINPUT 10000
#define WSIZE 32
#define NREADS 1000000

int main(int ac, char** av) {
	FILE *fIn, *fOut;
	int64_t i, j, nR, seqLen = 0;
	char *seq, c, toW;
	long *offset = NULL;

	if (ac != 3)
		terror("USE: reverseComplement seqFile.IN reverseComplementarySeq.OUT");

	/**
	 * Allocating memory for the sequence
	 * Fixed amount of memory, change it to loadSeqDB?
	 */
	if ((seq = (char*) malloc(SEQSIZE)) == NULL)
		terror("memory for Seq");

	if ((fIn = fopen(av[1], "rt")) == NULL)
		terror("opening IN sequence FASTA file");

	if ((fOut = fopen(av[2], "wt")) == NULL)
		terror("opening OUT sequence Words file");
	
	if ((offset = (long *) malloc(sizeof(long)*NREADS)) == NULL)
		terror("memory for offsets");

	for(i=0;i<NREADS;i++){
		offset[i]=0;
	}

	nR = 0;
	c = fgetc(fIn);
	while(!feof(fIn)){
		if(c == '>'){
			offset[nR++] = ftell(fIn)-1;
		}
		c = fgetc(fIn);
	}

	for(i=nR-1; i>=0; i--){
		fseek(fIn, offset[i], SEEK_SET);
		//READ and write header
		if(fgets(seq, READINPUT, fIn)==NULL){
			terror("Empty file");
		}
		fprintf(fOut, "%s", seq);
		//READ and write sequence
		c = fgetc(fIn);
		while(c != '>' && !feof(fIn)){
			if(isupper(c) || islower(c)){
				seq[seqLen++]=c;
			}
			c = fgetc(fIn);
		}
		for(j=seqLen-1; j >= 0; j--){
			switch(seq[j]){
				case 'A':
					toW = 'T';
					break;
				case 'C':
					toW = 'G';
					break;
				case 'G':
					toW = 'C';
					break;
				case 'T':
					toW = 'A';
					break;
				case 'U':
					toW = 'A';
					break;
				case 'a':
					toW = 't';
					break;
				case 'c':
					toW = 'g';
					break;
				case 'g':
					toW = 'c';
					break;
				case 't':
					toW = 'a';
					break;
				case 'u':
					toW = 'a';
					break;
				default:
					toW = seq[j];
					break;
			}
			fwrite(&toW, sizeof(char), 1, fOut);
		}
		toW='\n';
		fwrite(&toW, sizeof(char), 1, fOut);
		seqLen=0;
	}

	fclose(fIn);
	fclose(fOut);

	return 0;
}