diff chromeister/src/reverseComplement.c @ 1:3d1fbde7e0cc draft default tip

Deleted selected files

--- a/chromeister/src/reverseComplement.c	Wed Dec 12 07:18:40 2018 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,124 +0,0 @@
-/* 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.
-   [e-mail]
- */
-
-#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;
-}
-
-