int main(void) {
char s[MAX_LEN], t[MAX_LEN], val;
int i = 0;
while((val = getchar()) != '\n') s[i++] = val;
s[i] = '\0';
i = 0;
while((val = getchar()) != '\n') t[i++] = val;
t[i] = '\0';
edit_sequence(s, t);
return 0;
}
/*
* Enters a reading. This does not perform any linking of neighbours and
* updating of the contig. If an alignment buffer 'res' is non NULL then
* it is used as a list of edits. See the calign() code for details of
* the format for this buffer.
*
* It does however edit and enter the tags (on both the reading and
* consensus).
*
* Returns reading number for success, -1 for failure.
*/
int enter_reading(GapIO *io, SeqInfo *si, int comp, align_info *ai,
int contig, int position) {
GReadings r;
int reading;
char *name;
int start, end, length, alength;
char *seq = NULL;
int1 *conf = NULL;
int2 *opos = NULL;
anno_info *anno_r, *anno_c;
int anno_rl, anno_cl;
int retcode = -1;
int i;
/*
* Allocate
*/
io_init_reading(io, NumReadings(io)+1);
reading = NumReadings(io);
/*
* Write the reading name
*/
if (NULL == (name = read_sequence_name(si)))
goto end;
write_rname(io, reading, name);
/*
* length, start, end, sense
*/
length = si->length;
start = si->start;
end = si->end;
alength = length + 100;
/* Allocate temporary buffers */
seq = (char *)xmalloc(alength * sizeof(*seq));
conf = (int1 *)xmalloc(alength * sizeof(*conf));
opos = (int2 *)xmalloc(alength * sizeof(*opos));
if (!seq || !conf || !opos)
goto end;
/*
* Obtain the sequence, original positions, and confidence values.
*/
strcpy(seq, exp_get_entry(si->e, EFLT_SQ));
SeqInfo_opos(si, opos, length);
SeqInfo_conf(si, conf, length);
/*
* Complement if necessary
*/
if (comp)
io_complement_seq(&length, &start, &end, seq, conf, opos);
/*
* Load the tags into memory
*/
anno_r = create_anno_list(si, EFLT_TG, &anno_rl, length);
anno_c = create_anno_list(si, EFLT_TC, &anno_cl, 0);
/*
* Edit the sequence, consensus and tags
*/
if (ai)
edit_sequence(io, ai, &alength, &length, &start, &end,
&seq, &conf, &opos, contig,
comp, anno_r, anno_rl, anno_c, anno_cl);
/*
* write sequence to file
*/
if (io_write_seq(io, reading, &length, &start, &end, seq, conf, opos)) {
verror(ERR_WARN, "enter_reading",
"Problem writing new sequence to database: %s", name);
return -1;
}
/* Shouldn't this be in io_write_seq? */
gel_read(io, reading, r);
r.sequence_length = end - start - 1;
if (comp) {
io_length(io, reading) = -r.sequence_length;
r.sense = GAP_SENSE_REVERSE;
} else {
io_length(io, reading) = r.sequence_length;
r.sense = GAP_SENSE_ORIGINAL;
}
gel_write(io, reading, r);
/*
* write raw data info
*/
if (exp_Nentries(si->e, EFLT_LT) &&
exp_Nentries(si->e, EFLT_LN)) {
if (io_write_rd(io,
reading,
exp_get_entry(si->e, EFLT_LN),
strlen(exp_get_entry(si->e, EFLT_LN)),
exp_get_entry(si->e, EFLT_LT),
strlen(exp_get_entry(si->e, EFLT_LT)))) {
verror(ERR_WARN, "enter_reading",
"Problem writing raw data information to database: %s",
name);
return -1;
}
}
/*
* Write the tag data
*/
write_anno_list(io, anno_r, anno_rl, reading, 0, comp,
start, end, length);
write_anno_list(io, anno_c, anno_cl, -contig, position-1-r.start,
comp, start, end, length);
free_anno_list(anno_r, anno_rl);
free_anno_list(anno_c, anno_cl);
/*
* Add NoTes
*/
for(i = 0; i < exp_Nentries(si->e, EFLT_NT); i++) {
create_note_for_gel(io, reading,
arr(char *, si->e->entries[EFLT_NT], i));
}
/*
* write everything else
*/
retcode = add_seq_details(io, reading, si) ? -1 : reading;
end:
if (seq)
xfree(seq);
if (conf)
xfree(conf);
if (opos)
xfree(opos);
return retcode;
}
