/*
* Compute the visible statr position of a contig. This isn't just the extents
* of start_used / end_used in the bins as this can included invisible
* data such as cached consensus sequences.
*/
int contig_visible_start(GapIO *io, tg_rec crec) {
rangec_t *r;
contig_iterator *ci;
ci = contig_iter_new_by_type(io, crec, 1, CITER_FIRST | CITER_ISTART,
CITER_CSTART, CITER_CEND,
GRANGE_FLAG_ISANY);
if (!ci) {
contig_t *c = cache_search(io, GT_Contig, crec);
return c->start;
}
while (r = contig_iter_next(io, ci)) {
int v;
if ((r->flags & GRANGE_FLAG_ISMASK) == GRANGE_FLAG_ISCONS)
continue;
v = r->start;
contig_iter_del(ci);
return v;
}
contig_iter_del(ci);
return 0;
}
static void tag_shift_for_delete(GapIO *io, tg_rec crec, tg_rec srec,
int start, int end, int pos, tg_rec brec) {
contig_iterator *ci;
rangec_t *r;
contig_t *c = cache_search(io, GT_Contig, crec);;
//printf("< tag in seq %"PRIrec" at %d\n", srec, pos);
cache_incr(io, c);
ci = contig_iter_new_by_type(io, crec, 0, CITER_FIRST | CITER_ISTART,
start+pos, end, GRANGE_FLAG_ISANNO);
if (!ci) {
cache_decr(io, c);
return;
}
while ((r = contig_iter_next(io, ci))) {
range_t r2, *r_out;
anno_ele_t *a;
bin_index_t *bin;
if (r->pair_rec != srec)
continue;
bin_remove_item(io, &c, GT_AnnoEle, r->rec);
r2.start = (r->start > start+pos) ? r->start-1 : r->start;
r2.end = r->end-1;
r2.mqual = r->mqual;
r2.rec = r->rec;
r2.pair_rec = r->pair_rec;
r2.flags = r->flags;
if (r2.end < r2.start) {
/* Tag entirely removed now, it must have been on a pad */
a = cache_search(io, GT_AnnoEle, r->rec);
a = cache_rw(io, a);
cache_deallocate(io, a);
continue;
}
bin = bin_add_to_range(io, &c, brec, &r2, &r_out, NULL, 0);
a = cache_search(io, GT_AnnoEle, r->rec);
if (a->bin != bin->rec /*||
a->idx != r_out - ArrayBase(range_t, bin->rng)*/) {
/* Annotation moved bins */
a = cache_rw(io, a);
a->bin = bin->rec;
//a->bin_idx = r_out - ArrayBase(range_t, bin->rng);
}
}
cache_decr(io, c);
contig_iter_del(ci);
}
static void test_mode3(GapIO *io, int cnum, int xpos) {
rangec_t *r;
contig_iterator *ci;
ci = contig_iter_new(io, cnum, 0, CITER_FIRST, CITER_CSTART, CITER_CEND);
while (r = contig_iter_next(io, ci)) {
seq_t *s = get_seq(io, r->rec);
char name[256];
sprintf(name, "%.*s", s->name_len, s->name);
printf("%c%-22s\t%8d..%-8d\t%.*s\n",
"+-"[s->len<0], name, r->start, r->end, ABS(s->len), s->seq);
}
contig_iter_del(ci);
exit(0);
}
/*
* Removes all tags of specific types (hashed in h, or all if h == NULL)
* from a specified contig.
*
* Returns 0 on success
* -1 on failure
*/
static int delete_tag_single_contig(GapIO *io, tg_rec crec,
HashTable *h, int verbose) {
contig_iterator *ci;
rangec_t *r;
contig_t *c;
int ret = -1;
ci = contig_iter_new_by_type(io, crec, 1, CITER_FIRST,
CITER_CSTART, CITER_CEND,
GRANGE_FLAG_ISANNO);
if (!ci)
return -1;
if (!(c = cache_search(io, GT_Contig, crec))) {
contig_iter_del(ci);
return -1;
}
cache_incr(io, c);
while (NULL != (r = contig_iter_next(io, ci))) {
char t[5];
(void)type2str(r->mqual, t);
if (!h || HashTableSearch(h, t, 4)) {
anno_ele_t *e;
if (verbose)
vmessage("Removing anno %s #%"PRIrec"\tContig %s\t%d..%d\n",
t, r->rec, c->name, r->start, r->end);
if (bin_remove_item(io, &c, GT_AnnoEle, r->rec)) goto fail;
/* FIXME: Need to reclaim the GT_AnnoEle record itself */
}
}
ret = 0;
fail:
contig_iter_del(ci);
cache_decr(io, c);
return ret;
}
/*
* Scans through one or more contigs checking each reading for correct
* assembly. This is simply a check for misaligned data, not looking into
* cutoff data. (The gap4 method did this, but it hasn't yet been implemented
* in gap5).
*
* Returns -1 for failure, 0 for success.
*/
int check_assembly(GapIO *io, int num_contigs, contig_list_t *contigs,
int winsize, float maxperc, int ignore_N) {
int i, sc, count = 0, allocated = 0;
char *con;
tg_rec *reads = NULL, *conts = NULL;
int *score = NULL, *length = NULL, *pos = NULL;
for (i = 0; i < num_contigs; i++) {
tg_rec crec = contigs[i].contig;
contig_iterator *ci;
rangec_t *r;
int start = contigs[i].start, end = contigs[i].end;
if (NULL == (con = (char *)xmalloc(end-start+1)))
return -1;
calculate_consensus_simple(io, crec, start, end, con, NULL);
ci = contig_iter_new(io, crec, 0, CITER_FIRST, start, end);
while (NULL != (r = contig_iter_next(io, ci))) {
UpdateTextOutput();
sc = check_uassembly_single(io, con - start, crec, r,
maxperc, winsize, ignore_N);
if (count >= allocated) {
allocated = allocated ? allocated * 2 : 256;
reads = xrealloc(reads, allocated * sizeof(*reads));
conts = xrealloc(conts, allocated * sizeof(*conts));
score = xrealloc(score, allocated * sizeof(*score));
length = xrealloc(length, allocated * sizeof(*length));
pos = xrealloc(pos, allocated * sizeof(*pos));
if (!reads || !conts || !score || !length || !pos)
goto error;
}
if (sc > 0) {
reads[count] = r->rec;
score[count] = sc * 100;
pos[count] = r->start;
length[count] = r->end - r->start+1;
conts[count++] = crec;
}
}
contig_iter_del(ci);
xfree(con);
}
if (-1 == check_assembly_plot(io, reads, conts, score, pos, length, count))
goto error;
if (reads)
xfree(reads);
if (conts)
xfree(conts);
if (pos)
xfree(pos);
if (length)
xfree(length);
if (score)
xfree(score);
return 0;
error:
if (reads)
xfree(reads);
if (conts)
xfree(conts);
if (pos)
xfree(pos);
if (length)
xfree(length);
if (score)
xfree(score);
return -1;
}
/**
* Builds and returns MALIGN from a Gap5 IO handle for the contig 'cnum'.
*/
MALIGN *build_malign(GapIO *io, tg_rec cnum, int start, int end) {
CONTIGL *contig, *first_contig = NULL, *last_contig = NULL;
int i, j;
contig_iterator *citer;
rangec_t *r;
/* Expand start and end to the range covered by seqs overlapping
* start .. end
*/
{
seq_t *s;
citer = contig_iter_new(io, cnum, 0,
CITER_FIRST | CITER_ICLIPPEDSTART,
start, start);
r = contig_iter_next(io, citer);
if (r) {
s = cache_search(io, GT_Seq, r->rec);
start = ((s->len < 0) ^ r->comp)
? r->end - s->right - 2
: r->start + s->left - 2;
}
contig_iter_del(citer);
}
{
seq_t *s;
citer = contig_iter_new(io, cnum, 0,
CITER_LAST | CITER_ICLIPPEDEND,
end, end);
r = contig_iter_next(io, citer);
if (r) {
s = cache_search(io, GT_Seq, r->rec);
end = ((s->len < 0) ^ r->comp)
? r->end - s->left + 2
: r->start + s->right + 2;
}
contig_iter_del(citer);
}
//printf("Generating data for %d..%d\n", start, end);
/* Generate contigl linked list */
//citer = contig_iter_new(io, cnum, 1, CITER_FIRST, CITER_CSTART, CITER_CEND);
citer = contig_iter_new(io, cnum, 0, CITER_FIRST, start, end);
while ((r = contig_iter_next(io, citer))) {
seq_t *s, *sorig;
char *seq;
int len;
assert((r->flags & GRANGE_FLAG_ISMASK) == GRANGE_FLAG_ISSEQ);
contig = create_contig_link();
contig->id = r->rec;
contig->mseg = create_mseg();
sorig = s = cache_search(io, GT_Seq, r->rec);
/* Check for out-of-bounds clip points. It shouldn't happen, but
gap5 databases have been seen with this problem, and we
don't want to crash if there are any. */
if (s->left < 1) s->left = 1;
if (s->right > ABS(s->len)) s->right = ABS(s->len);
/* Fix reads of zero length */
if (s->right < s->left) {
sorig = s = cache_rw(io, s);
s->right = s->left;
if (s->right > ABS(s->len))
s->left = s->right = ABS(s->len);
}
if ((s->len < 0) ^ r->comp) {
s = dup_seq(s);
complement_seq_t(s);
}
len = s->right - s->left + 1;
if (NULL == (seq = malloc(len+1)))
return NULL;
for (j = 0, i = s->left-1; i < s->right; i++, j++) {
/* Protect against the sequence containing "."; our pad sym */
if (s->seq[i] == '.')
seq[j] = 'N';
else
seq[j] = s->seq[i];
}
seq[j] = 0;
init_mseg(contig->mseg, seq, len, r->start-1 + s->left-1);
contig->mseg->comp = (s != sorig);
if (last_contig) {
last_contig->next = contig;
} else {
first_contig = contig;
}
last_contig = contig;
if (s != sorig)
free(s);
}
contig_iter_del(citer);
/* for 454 data -6 to -10 seem to work fine */
return contigl_to_malign(first_contig, -7, -7);
}
/*
* find matches between user entered sequence string and contig list with
* a minimum match of mis_match
*/
int
StringMatch(GapIO *io, /* in */
int num_contigs, /* in */
contig_list_t *contig_array, /* in */
char **cons_array, /* in */
char *string, /* in */
float mis_fmatch, /* in */
int *pos1, /* out */
int *pos2, /* out */
int *score, /* out */
int *length, /* out */
tg_rec *c1, /* out */
tg_rec *c2, /* out */
int max_matches, /* in */
int consensus_only, /* in */
int cutoff_data) /* in */
{
int n_matches = 0;
int i, j, k, c;
int mis_match;
int seq_len;
int orig;
int res, too_many = 0;
char *cons_match;
char title[1024];
char name1[10];
int max_imatches = max_matches;
size_t stringlen = strlen(string);
if (NULL == (cons_match = (char *)xmalloc(stringlen + 1)))
return -1;
/* convert percentage mis-matches into number of mis matches */
mis_match = strlen(string) - (ceil(strlen(string) * mis_fmatch / 100.));
/* complement string */
for (c = 0; c < 2; c++) {
if (c == 1)
complement_seq(string, stringlen);
for (i = 0; i < num_contigs; i++) {
rangec_t *r;
contig_iterator *ci = NULL;
/*
* Consensus first time through loop.
* Sequences in that contig on subsequent loops.
*/
for (r = (rangec_t *)1; r; r = contig_iter_next(io, ci)) {
char *seq;
seq_t *s = NULL;
if (ci == 0) {
/* First time through is consensus */
seq = cons_array[i];
seq_len = strlen(cons_array[i]);
} else {
/* Subsequent times r is valid (not 1) and a sequence */
if ((r->flags & GRANGE_FLAG_ISMASK) !=
GRANGE_FLAG_ISSEQ)
continue;
s = cache_search(io, GT_Seq, r->rec);
if (cutoff_data) {
seq = s->seq;
seq_len = ABS(s->len);
} else {
seq = &s->seq[s->left-1];
seq_len = s->right - s->left+1;
}
}
orig = n_matches;
res = inexact_pad_match(seq, seq_len, string,
stringlen, mis_match,
&pos1[n_matches], &score[n_matches],
max_imatches);
if (res == -2)
return -1;
if (res < 0) {
verror(ERR_WARN, "find_oligos", "Too many matches");
too_many = 1;
res = max_imatches;
}
n_matches += res;
max_imatches -= res;
for (j = k = orig; j < n_matches; j++) {
int padded_len;
c1[j] = contig_array[i].contig;
if (c == 0) {
c2[j] = contig_array[i].contig;
} else {
c2[j] = -contig_array[i].contig;
}
/*
* remove pads such that the final length of cons_match is
* of length length[j]
*/
padded_len =
depad_seq_len(cons_match, &seq[pos1[j]-1], stringlen);
if (ci) {
if (cutoff_data) {
pos1[j] += r->start-1;
} else {
pos1[j] += r->start-1 + s->left-1;
}
}
length[j] = padded_len;
/* Adjust for searching in a sub-range of the contig */
if (!ci)
pos1[j] += contig_array[i].start-1;
pos2[j] = pos1[j];
/*
* The searching above may find hits outside of
* contig_array[i].start and contig_array[i].end.
*
* This happens if we search sequences and the
* sequence overlaps the desired range, but has a
* hit outside of the desired range.
*
* Rather than complicate the above code, we post
* filter these false hits here.
*/
if (pos1[j] >= contig_array[i].start &&
pos1[j] <= contig_array[i].end) {
sprintf(name1, "%"PRIrec"", io_clnbr(io, ABS(c1[j])));
sprintf(title, "Match found with contig #%"PRIrec
" read #%"PRIrec
" in the %c sense",
contig_array[i].contig,
ci ? r->rec : 0,
c2[j] > 0 ? '+' : '-');
list_alignment(string, cons_match, "oligo", name1, 1,
pos1[j], title);
/*
* Copy it from *[j] to *[k].
* This code REALLY needs to be using structs!
* This is foul.
*/
pos1 [k] = pos1 [j];
pos2 [k] = pos2 [j];
c1 [k] = c1 [j];
c2 [k] = c2 [j];
length[k] = length[j];
score [k] = score [j];
k++;
}
}
n_matches -= j-k;
max_imatches += j-k;
if (too_many)
break;
if (consensus_only)
break;
if (!ci) {
ci = contig_iter_new(io,
contig_array[i].contig,
0 /*autoextend */,
CITER_FIRST,
contig_array[i].start,
contig_array[i].end);
if (!ci)
break;
}
}
if (too_many)
break;
}
if (too_many)
break;
}
xfree(cons_match);
vmessage("Number of matches found %d \n", n_matches);
return n_matches;
}
