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/*
* =============================================================================
*
* Filename: SeqIO.c
*
* Description:
*
* Revision: none
* Compiler: gcc 4.3.2 or above
*
* Author: Chang Yu (yc), yuchang@genomics.org.cn
* Company: BGI Shenzhen
* CopyRight: Copyright (c) 2009, BGI Shenzhen
*
* =============================================================================
*/
#include "SeqIO.h"
extern unsigned char charMap[256];
extern unsigned char complementMap[256];
extern const char ambiguityCount[16];
int CheckFast (int fd) {
char c;
if (read(fd, &c, 1)>0) {
lseek(fd, -1, SEEK_CUR);
if (c == '>') return FASTA;
else if (c == '@') return FASTQ;
else {
fprintf(stderr, "File Error: unrecognized file\n");
close(fd);
exit(EXIT_FAILURE);
}
}
return FASTA;
}
int fasta(FILE *fp, seq_t *seq, const int CONV){
int l, max, ns;
int c;
char *p, *q;
l = ns = 0;
max=seq->max;
while (!feof(fp) && getc(fp)!= (int)'>');
if (feof(fp)) return -1;
p = seq->name;
while ((c= getc(fp)) != ' ' && c != '\r' && c != '\t' && c != '\n' && ++l < MAX_NAME_LEN) *p++ = c;
/*parse RG ID for SAM
if(o->SAM){
if(p[l-1] == '1' && p[l-2] == '/') {r->RG_ID = 1; l-=2;}
else if(p[l-1] == '2' && p[l-2] == '/'){r->RG_ID = 2; l-=2;}
else {seq->RG_ID = 1;}
}
//*/
*p = '\0';
while (c != '\n') c = (char) getc(fp);
if (feof(fp)) {
fprintf(stderr, "\nFile Error: unexpected feof\n");
exit(EXIT_FAILURE);
}
l = 0;
p=seq->seq; q=seq->rc;
while ((c = getc(fp)) != '>' && !feof(fp)) {
if (c != '\n' && c != '\r') {
if (l >= max) {
max += QUERY_LEN;
seq->seq = (char *)realloc(seq->seq, sizeof(char)* max);
seq->rc = (char *)realloc(seq->rc, sizeof(char)* max);
seq->qual = (char *)realloc(seq->qual, sizeof(char) * max);
p = seq->seq + l;
q = seq->rc + l;
}
if (ambiguityCount[charMap[c]] != 1) {
*p++ = charMap['G'];
*q++ = complementMap['G'];
ns++;
} else {
*p++ = charMap[c];
*q++ = complementMap[c];
}
seq->qual[l] = 'h';
l++;
}
}
seq->qual[l] = *p = *q = '\0';
seq->l = l;
seq->max = max;
seq->ns = ns;
if (c == '>') ungetc(c,fp);
return l;
} /* ----- end of function fasta ----- */
int fastq (FILE *fp, seq_t *seq, const int CONV) {
#ifdef DEBUG
// fprintf(stderr, "get read\n");
#endif
int l, max, ns;
int c;
char *p;
l = ns = 0;
max = seq->max;
while (!feof(fp) && getc(fp)!= '@');
if (feof(fp)) return -1;
l = 0;
p=seq->name;
while ((c = getc(fp)) != '\t' && c != ' ' && c != '\n' && c != '\r' && l++ < MAX_NAME_LEN) *p++ = c;
*p = '\0';
// fprintf(stderr, "%s\n", seq->name);
/* RG ID for SAM
if(o->SAM){
if(p[l-1] == '1' && p[l-2] == '/') {r->RG_ID = 1; l-=2;}
else if(p[l-1] == '1' && p[l-2] == '/'){r->RG_ID = 2; l-=2;}
else {r->RG_ID = 1;}
}
//*/
while (c != '\n') c = getc(fp);
if (feof(fp)) {
fprintf(stderr, "\nFile Error: unexpected feof\n");
exit(EXIT_FAILURE);
}
l = 0;
// p = seq->seq; q = seq->rc;
while ((c = getc(fp)) != '+' && !feof(fp)) {
if (c != '\n' && c != '\r') {
if (l >= max) {
max += QUERY_LEN;
seq->seq = (char *)realloc(seq->seq, sizeof(char)*max);
seq->rc = (char *)realloc(seq->rc, sizeof(char)* max);
seq->qual = (char *)realloc(seq->qual, sizeof(char)*max);
// fprintf(stderr, "%d\n", max);
// p = seq->seq + l;
// q = seq->rc + l;
}
// fprintf(stdout, "%c", c);
if(ambiguityCount[charMap[c]] == 1){
seq->seq[l] = charMap[c];
seq->rc[l++] = complementMap[c];
}else{
seq->seq[l] = charMap['G'];
seq->rc[l++] = complementMap['G'];
ns++;
}
}
}
// *p = '\0'; *q = '\0';
// fprintf(stderr, "\n");
// for(j=0; j<l;j++)fprintf(stderr, "%d", seq->seq[j]);
// fprintf(stderr, "\n");
seq->l = l;
// fprintf(stdout, "\n");
while (!feof(fp) && (c= getc(fp))!= '\n');
if (feof(fp)) {
fprintf(stderr, "\nFile Error: unexpected feof\n");
return 0;
}
l = 0;
p = seq->qual;
while ((c = (char) getc(fp)) != '\n' && c != '\r' && !feof(fp)) {
if (l > max) {
max += QUERY_LEN;
seq->qual = (char *)realloc(seq->qual, sizeof(char)*max);
p=seq->qual; p+=l;
}
*p++ = c;
l++;
}
*p = '\0';
if (l != seq->l) {
fprintf(stderr, "Length Error: incompitable seq and qual length\n");
fprintf(stderr, " %s\n", seq->name);
return 0;
}
if (c == '@') ungetc(c,fp);
seq->max = max;
seq->ns = ns;
// fprintf(stderr, "%d:%d\n", seq->l, l);
return seq->l;
}
/* test
int main(int argc, char *argv[]){
int fd = open(argv[1])
return EXIT_SUCCESS;
}
//*/
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