int edview_search_cons_discrep(edview *xx, int dir, int strand, char *value) {
int start, end;
int found = 0, at_end = 0;
int fpos, i;
double qval = atof(value);
consensus_t cons[WIN_WIDTH+1];
contig_t *c;
/* Set initial start positions */
if (dir) {
start = xx->cursor_apos + (dir ? 1 : -1);
end = start + (WIN_WIDTH-1);
} else {
end = xx->cursor_apos + (dir ? 1 : -1);
start = end - (WIN_WIDTH-1);
}
fpos = xx->cursor_apos;
/* Loop WIN_WIDTH block at a time */
c = cache_search(xx->io, GT_Contig, xx->cnum);
cache_incr(xx->io, c);
do {
calculate_consensus(xx->io, xx->cnum, start, end, cons);
if (dir) {
for (i = 0; i < WIN_WIDTH; i++) {
if (cons[i].discrep >= qval) {
found = 1;
break;
}
}
} else {
for (i = WIN_WIDTH-1; i; i--) {
if (cons[i].discrep >= qval) {
found = 1;
break;
}
}
}
if (found) {
fpos = start + i;
break;
}
/* Next search region - overlapping by patlen+pads */
if (dir) {
start += WIN_WIDTH;
end += WIN_WIDTH;
if (start > c->end)
at_end = 1;
} else {
start -= WIN_WIDTH;
end -= WIN_WIDTH;
if (end < c->start)
at_end = 1;
}
} while (!at_end);
cache_decr(xx->io, c);
if (found) {
edSetCursorPos(xx, GT_Contig, xx->cnum, fpos, 1);
return 0;
}
return -1;
}
/*
* ----------------------------------------------------------------------
* Remove Pad Columns. Sometimes we don't want to realign data, we just
* want to remove (aligned) columns of pads.
* ----------------------------------------------------------------------
*/
int remove_pad_columns(GapIO *io, int ncontigs, contig_list_t *contigs,
int percent_pad, int quiet) {
int i;
consensus_t *cons = NULL;
size_t max_alloc = 0;
for (i = 0; i < ncontigs; i++) {
tg_rec cnum = contigs[i].contig;
size_t len, j;
int ndel = 0;
contig_t *c;
if (!quiet) {
vmessage("Processing contig %d of %d (#%"PRIrec")\n",
i+1, ncontigs, cnum);
UpdateTextOutput();
}
c = cache_search(io, GT_Contig, cnum);
if (!c)
return -1;
cache_incr(io, c);
len = contigs[i].end - contigs[i].start + 1;
if (max_alloc < len) {
max_alloc = len;
cons = realloc(cons, max_alloc * sizeof(*cons));
}
if (0 != calculate_consensus(io, cnum,
contigs[i].start, contigs[i].end,
cons)) {
free(cons);
cache_decr(io, c);
return -1;
}
for (j = 0; j < len; j++) {
if (cons[j].call != 4)
continue;
if (100 * cons[j].counts[4] / cons[j].depth < percent_pad)
continue;
if (!quiet)
vmessage(" Removing column %d %d%% pad (%d of %d), conf. %f)\n",
(int)j+contigs[i].start,
100 * cons[j].counts[4] / cons[j].depth,
cons[j].counts[4], cons[j].depth,
cons[j].scores[cons[j].call]);
contig_delete_base(io, &c, contigs[i].start + j - ndel);
ndel++;
}
cache_decr(io, c);
}
if (cons)
free(cons);
return 0;
}
