void mexFunction(int nlhs, mxArray *plhs[], int nrhs, const mxArray *prhs[]){
file_t *fp;
char *fn=NULL;
int start=0, howmany=0;
switch(nrhs){
case 3:
start=(long)mxGetScalar(prhs[2]);//starting block to read. matlab index.
case 2:
howmany=(long)mxGetScalar(prhs[1]);//do not break
case 1:
fn=mx2str(prhs[0]);
break;
default:
usage();
}
if(howmany>0){
if(start>0){
start--;//convert to C index.
}
if(start<0){
start=0;
}
}
fp=zfopen(fn,"rb");
if(!fp){
perror("zfopen");
error("Unable to open file: %s\n", fn);
return;
}
free(fn);
switch(nlhs){
case 0:
case 1:
plhs[0]=readdata(fp, NULL, start, howmany); break;
case 2:
plhs[0]=readdata(fp, &plhs[1], start, howmany); break;
default:
usage();
}
if(start==0 && howmany==0){
int res=zfeof(fp);
if(res){
warning("There is unread data: res=%d\n", res);
}
}
zfclose(fp);
}
int fastaq_next(zfp *fp, fastq_entry_t *e) {
char line[BLK_SIZE];
size_t l, pos = 0;
int discard = 0, more;
/* Skip blank lines */
line[BLK_SIZE - 1] = '*';
do {
if (NULL == zfgets(line, BLK_SIZE, fp)) return 1;
e->line++;
} while (*line == '\n');
/* Read name */
for (;;) {
if (!discard) {
char *start = line, *cp;
if (0 == pos) { /* Check first char */
if (e->header) {
if (*line != e->header) {
verror(ERR_WARN, "fastaq_next",
"Error: sequence name does not start with '%c' "
"at %s line %lu.",
e->header, e->fn, e->line);
return -1;
}
} else {
if (*line != HDR_FASTA && *line != HDR_FASTQ) {
verror(ERR_WARN, "fastaq_next",
"Error: sequence name does not start with "
"'%c' or '%c' at %s line %lu.",
HDR_FASTA, HDR_FASTQ, e->fn, e->line);
return -1;
} else {
e->header = *line;
e->seq_delimiter = (*line == HDR_FASTA
? DELIM_FASTA : DELIM_FASTQ);
}
}
start++;
}
cp = start;
while (*cp && !isspace(*cp)) cp++;
if (e->max_name_len < pos + cp - start + 1) {
if (0 != grow_char_string(&e->name, &e->max_name_len,
pos + cp - start + 1)) {
return -1;
}
}
memcpy(e->name + pos, start, cp - start);
pos += cp - start;
e->name[pos] = '\0';
if (isspace(*cp)) discard = 1;
}
if (line[BLK_SIZE - 1] == '*' || line[BLK_SIZE - 2] == '\n') break;
line[BLK_SIZE - 1] = '*';
if (NULL == zfgets(line, BLK_SIZE, fp)) {
verror(ERR_WARN, "fastaq_next",
"Error: Unexpected end-of-file while reading sequence name "
"at %s line %lu", e->fn, e->line);
return -1;
}
}
if (*e->name == '\0') {
verror(ERR_WARN, "fastaq_next",
"Error: Sequence entry with no name at %s line %lu",
e->fn, e->line);
return -1;
}
/* Sequence */
e->seq_len = 0;
more = 0;
while (!zfeof(fp) && (zfpeek(fp) != e->seq_delimiter || more)) {
char *src = line, *dest;
if (NULL == zfgets(line, BLK_SIZE, fp)) break;
if (!more) e->line++;
l = strlen(line);
if (0 == l) {
verror(ERR_WARN, "fastaq_next",
"Error: Unexpected NUL byte at %s line %lu\n",
e->fn, e->line);
return -1;
}
if (e->max_seq_len < e->seq_len + l + 1) {
if (0 != grow_char_string(&e->seq, &e->max_seq_len,
e->seq_len + l + 1)) {
return -1;
}
}
for (dest = e->seq + e->seq_len; *src; src++) {
if (!isspace(*src)) *dest++ = *src;
}
e->seq_len = dest - e->seq;
more = line[l - 1] != '\n';
}
if (e->seq) e->seq[e->seq_len] = '\0';
/* Done if fasta */
if (e->header != HDR_FASTQ) return 0;
/* + line: skip */
line[BLK_SIZE - 1] = '*'; /* Sentinal */
if (NULL == zfgets(line, BLK_SIZE, fp) || *line != DELIM_FASTQ) {
verror(ERR_WARN, "fastaq_next",
"Error: Expected '%c' got '%c' reading fastq entry %.1000s",
DELIM_FASTQ, *line, e->name);
return -1;
}
e->line++;
while (line[BLK_SIZE - 1] != '*' && line[BLK_SIZE - 2] != '\n') {
line[BLK_SIZE - 1] = '*';
if (NULL == zfgets(line, BLK_SIZE, fp))
return -1; /* eof */
}
/* Read quality, no more than e->seq_len chars */
pos = 0;
more = 0;
while (pos < e->seq_len && !zfeof(fp)) {
char *src = line, *dest;
if (NULL == zfgets(line, BLK_SIZE, fp))
break;
if (!more) e->line++;
more = (line[BLK_SIZE - 1] != '*' && line[BLK_SIZE - 2] != '\n');
l = strlen(line);
if (e->max_qual_len < pos + l + 1) {
if (0 != grow_char_string(&e->qual, &e->max_qual_len, pos + l + 1))
return -1;
}
for (dest = e->qual + pos; *src; src++) {
if (!isspace(*src)) *dest++ = *src;
}
pos = dest - e->qual;
}
if (e->qual)
e->qual[pos] = '\0';
if (pos != e->seq_len) {
verror(ERR_WARN, "fastaq_next",
"Error: differing number of sequence and quality "
"characters for entry '%.1000s' at %s line %lu",
e->name, e->fn, e->line);
return -1;
}
return 0;
}
