static st32 mprint(RMagic *ms, struct r_magic *m) {
ut64 v;
float vf;
double vd;
ut64 t = 0;
char *buf = NULL;
union VALUETYPE *p = &ms->ms_value;
switch (m->type) {
case FILE_BYTE:
v = file_signextend(ms, m, (ut64)p->b);
switch (check_fmt(ms, m)) {
case -1:
return -1;
case 1:
buf = malloc (2);
if (snprintf (buf, 2, "%c", (ut8)v)<0) {
free (buf);
return -1;
}
if (file_printf (ms, R_MAGIC_DESC, buf) == -1) {
free (buf);
return -1;
}
break;
default:
if (file_printf(ms, R_MAGIC_DESC, (ut8) v) == -1)
return -1;
break;
}
t = ms->offset + sizeof(char);
break;
case FILE_SHORT:
case FILE_BESHORT:
case FILE_LESHORT:
v = file_signextend (ms, m, (ut64)p->h);
switch (check_fmt (ms, m)) {
case -1:
return -1;
case 1:
buf = malloc (32);
if (snprintf (buf, 32, "%hu", (unsigned short)v) < 0) {
free (buf);
return -1;
}
if (file_printf(ms, R_MAGIC_DESC, buf) == -1) {
free (buf);
return -1;
}
break;
default:
if (file_printf(ms, R_MAGIC_DESC, (unsigned short) v) == -1)
return -1;
break;
}
t = ms->offset + sizeof(short);
break;
case FILE_LONG:
case FILE_BELONG:
case FILE_LELONG:
case FILE_MELONG:
v = file_signextend(ms, m, (ut64)p->l);
switch (check_fmt(ms, m)) {
case -1:
return -1;
case 1:
buf = malloc (32);
if (snprintf (buf, 32, "%u", (ut32)v) < 0) {
free (buf);
return -1;
}
if (file_printf(ms, R_MAGIC_DESC, buf) == -1) {
free (buf);
return -1;
}
break;
default:
if (file_printf(ms, R_MAGIC_DESC, (ut32) v) == -1)
return -1;
break;
}
t = ms->offset + sizeof(st32);
break;
case FILE_QUAD:
case FILE_BEQUAD:
case FILE_LEQUAD:
v = file_signextend(ms, m, p->q);
if (file_printf(ms, R_MAGIC_DESC, (ut64) v) == -1)
return -1;
t = ms->offset + sizeof(ut64);
break;
case FILE_STRING:
case FILE_PSTRING:
case FILE_BESTRING16:
case FILE_LESTRING16:
if (m->reln == '=' || m->reln == '!') {
if (file_printf (ms, R_MAGIC_DESC, m->value.s) == -1)
return -1;
t = ms->offset + m->vallen;
}
else {
if (*m->value.s == '\0')
p->s[strcspn (p->s, "\n")] = '\0';
if (file_printf (ms, R_MAGIC_DESC, p->s) == -1)
return -1;
t = ms->offset + strlen (p->s);
if (m->type == FILE_PSTRING)
t++;
}
break;
case FILE_DATE:
case FILE_BEDATE:
case FILE_LEDATE:
case FILE_MEDATE:
if (file_printf(ms, R_MAGIC_DESC, file_fmttime(p->l, 1)) == -1)
return -1;
t = ms->offset + sizeof(time_t);
break;
case FILE_LDATE:
case FILE_BELDATE:
case FILE_LELDATE:
case FILE_MELDATE:
if (file_printf(ms, R_MAGIC_DESC, file_fmttime(p->l, 0)) == -1)
return -1;
t = ms->offset + sizeof(time_t);
break;
case FILE_QDATE:
case FILE_BEQDATE:
case FILE_LEQDATE:
if (file_printf(ms, R_MAGIC_DESC, file_fmttime((ut32)p->q, 1))
== -1)
return -1;
t = ms->offset + sizeof(ut64);
break;
case FILE_QLDATE:
case FILE_BEQLDATE:
case FILE_LEQLDATE:
if (file_printf(ms, R_MAGIC_DESC, file_fmttime((ut32)p->q, 0))
== -1)
return -1;
t = ms->offset + sizeof(ut64);
break;
case FILE_FLOAT:
case FILE_BEFLOAT:
case FILE_LEFLOAT:
vf = p->f;
switch (check_fmt(ms, m)) {
case -1:
return -1;
case 1:
buf = malloc (32);
if (snprintf (buf, 32, "%g", vf) < 0) {
free (buf);
return -1;
}
if (file_printf (ms, R_MAGIC_DESC, buf) == -1) {
free (buf);
return -1;
}
break;
default:
if (file_printf(ms, R_MAGIC_DESC, vf) == -1)
return -1;
break;
}
t = ms->offset + sizeof(float);
break;
case FILE_DOUBLE:
case FILE_BEDOUBLE:
case FILE_LEDOUBLE:
vd = p->d;
switch (check_fmt(ms, m)) {
case -1:
return -1;
case 1:
buf = malloc (32);
if (snprintf (buf, 32, "%g", vd) < 0) {
free (buf);
return -1;
}
if (file_printf (ms, R_MAGIC_DESC, buf) == -1) {
free (buf);
return -1;
}
break;
default:
if (file_printf(ms, R_MAGIC_DESC, vd) == -1)
return -1;
break;
}
t = ms->offset + sizeof(double);
break;
case FILE_REGEX: {
char *cp;
int rval;
cp = strdupn((const char *)ms->search.s, ms->search.rm_len);
if (cp == NULL) {
file_oomem(ms, ms->search.rm_len);
return -1;
}
rval = file_printf(ms, R_MAGIC_DESC, cp);
free(cp);
if (rval == -1)
return -1;
if ((m->str_flags & REGEX_OFFSET_START))
t = ms->search.offset;
else
t = ms->search.offset + ms->search.rm_len;
break;
}
case FILE_SEARCH:
if (file_printf(ms, R_MAGIC_DESC, m->value.s) == -1)
return -1;
if ((m->str_flags & REGEX_OFFSET_START))
t = ms->search.offset;
else t = ms->search.offset + m->vallen;
break;
case FILE_DEFAULT:
if (file_printf(ms, R_MAGIC_DESC, m->value.s) == -1)
return -1;
t = ms->offset;
break;
default:
file_magerror(ms, "invalid m->type (%d) in mprint()", m->type);
return -1;
}
free (buf);
return(t);
}
/*cut the reads from the string and process them one by one*/
void read_process (bloom * bl, Queue * info, Queue * tail, F_set * File_head, float sampling_rate, float tole_rate, char mode, char fmt_type)
{
char *start_point = info->location;
char *next_job = NULL, *temp = NULL, *previous_point = NULL, *temp_next = NULL;
int result = 0;
next_job = check_fmt (info, tail, start_point, fmt_type);
// make sure it can handle DOS and Unix format ('\r\n' and '\n')
// XXX: what about OSX sinle '\n' ('a0' in hexa)?
if (next_job == NULL)
return;
while (start_point != next_job)
{
if (mode == 'c')
{
if (sampling_rate<1)
temp = jump (start_point, fmt_type, sampling_rate);
else
temp = start_point;
// function for fast/proportional scan
if (start_point != temp)
{
start_point = temp;
continue;
}
}
// skip to the next read if needed
#pragma omp atomic
File_head->reads_num++;
// atomic process for summing reads number
previous_point = start_point;
start_point = get_right_sp (start_point, fmt_type);
// skip the ID line
if (fmt_type == '@')
{
//identify read as fastq format read and pass it to fastq_read_check to process
result = fastq_read_check (start_point, strchr (start_point, '\n') - start_point, 'n', bl, tole_rate, File_head);
start_point = strchr (start_point, '\n') + 1;
start_point = strchr (start_point, '\n') + 1;
start_point = strchr (start_point, '\n') + 1;
}
else
{
temp_next = strchr(start_point+1,'>');
if (temp_next == NULL)
temp_next = next_job;
//identify read as fasta format read and pass it to fasta_read_check to process
result = fasta_read_check (start_point, temp_next-start_point, 'n', bl, tole_rate, File_head);
start_point = temp_next;
}
if (result>0)
{
#pragma omp atomic
File_head->reads_contam++;
if (mode == 'r')
{
#pragma omp critical
{
memcpy(_contam,previous_point,start_point-previous_point);
_contam+=(start_point-previous_point);
}
}
}
else
{
if (mode == 'r')
{
#pragma omp critical
{
memcpy(_clean,previous_point,start_point-previous_point);
_clean+=(start_point-previous_point);
}
}
}
} // outside while
}
