/* Debug functions that don't use curses - handy for valgrind testing */
static void test_mode(GapIO *io, contig_t **c, int xpos) {
rangec_t *r;
int nr, i;
r = contig_seqs_in_range(io, c, xpos, xpos+79, CSIR_SORT_BY_X, &nr);
for (i = 0; i < nr; i++) {
seq_t *s = get_seq(io, r[i].rec);
printf("%.*s: range %d..%d seq %d+%d st=%d en=%d %.*s\n",
s->name_len, s->name,
r[i].start, r[i].end,
s->pos, s->len,
s->left, s->right,
ABS(s->len), s->seq);
s = dup_seq(s);
complement_seq_t(s);
printf("%.*s: range %d..%d seq %d+%d st=%d en=%d %.*s\n",
s->name_len, s->name,
r[i].start, r[i].end,
s->pos, s->len,
s->left, s->right,
ABS(s->len), s->seq);
}
gio_close(io);
system("ps lx | grep g_iotest | grep -v grep");
exit(0);
}
/*
* Attempt to find edits. It's not 100% reliable, but works for most cases.
* We look for lowercase bases and confidence 100 and 0 (if not N).
* We cannot find deleted bases though.
*/
int edview_search_edit(edview *xx, int dir, int strand, char *value) {
int start, end;
contig_iterator *iter;
rangec_t *(*ifunc)(GapIO *io, contig_iterator *ci);
rangec_t *r;
int best_pos, found = 0;
int fpos;
tg_rec fseq;
if (dir) {
start = xx->cursor_apos + 1;
end = CITER_CEND;
iter = contig_iter_new(xx->io, xx->cnum, 1,
CITER_FIRST | CITER_ISTART,
start, end);
ifunc = contig_iter_next;
best_pos = INT_MAX;
} else {
start = CITER_CSTART;
end = xx->cursor_apos -1;
iter = contig_iter_new(xx->io, xx->cnum, 1,
CITER_LAST | CITER_IEND,
start, end);
ifunc = contig_iter_prev;
best_pos = INT_MIN;
}
if (!iter)
return -1;
while ((r = ifunc(xx->io, iter))) {
seq_t *s, *sorig;
char *seq, *qual;
int seq_len, comp, off = 0, i;
if (found && dir && r->start > best_pos)
break;
if (found && !dir && r->end < best_pos)
break;
if (NULL == (s = sorig = cache_search(xx->io, GT_Seq, r->rec)))
break;
if (r->comp ^ (s->len < 0)) {
s = dup_seq(s);
complement_seq_t(s);
}
seq = s->seq;
qual = s->conf;
seq_len = ABS(s->len);
if (r->start < start) {
off = start - r->start;
seq += off;
qual += off;
seq_len -= off;
}
for (i = 0; i < seq_len; i++) {
if (islower(seq[i]) ||
qual[i] == 100 ||
(qual[i] == 0 && seq[i] != 'N' && seq[i] != '-'
&& seq[i] != '*')) {
int pos = r->start + i + off;
if (dir) {
if (best_pos > pos && pos > xx->cursor_apos) {
found = 1;
best_pos = pos;
fpos = i + off;
fseq = r->rec;
}
break;
} else {
if (best_pos < pos && pos < xx->cursor_apos) {
found = 1;
best_pos = pos;
fpos = i + off;
fseq = r->rec;
}
}
}
}
if (s != sorig)
free(s);
}
if (found) {
edSetCursorPos(xx, fseq == xx->cnum ? GT_Contig : GT_Seq,
fseq, fpos, 1);
}
contig_iter_del(iter);
return found ? 0 : -1;
}
int edview_search_sequence(edview *xx, int dir, int strand, char *value) {
int mismatches = 0; /* exact match */
int where = 2; /* consensus */
char *p;
int start, end;
int patlen;
char *uppert, *upperb;
int found = 0, at_end = 0;
tg_rec fseq;
int fpos, i, j;
contig_t *c;
contig_iterator *iter;
rangec_t *(*ifunc)(GapIO *io, contig_iterator *ci);
rangec_t *r;
int best_pos;
if (dir) {
start = xx->cursor_apos + 1;
end = CITER_CEND;
iter = contig_iter_new(xx->io, xx->cnum, 1,
CITER_FIRST | CITER_ISTART,
start, end);
ifunc = contig_iter_next;
best_pos = INT_MAX;
} else {
start = CITER_CSTART;
end = xx->cursor_apos -1;
iter = contig_iter_new(xx->io, xx->cnum, 1,
CITER_LAST | CITER_IEND,
start, end);
ifunc = contig_iter_prev;
best_pos = INT_MIN;
}
if (!iter)
return -1;
/*
* Parse value search string. It optionally includes two extra params
* separated by #. Ie:
* <string>#<N.mismatches>#<where>.
* <where> is 1 for readings, 2 for consensus, 3 for both.
*/
if (p = strchr(value, '#')) {
mismatches = atoi(p+1);
*p = 0;
if (p = strchr(p+1, '#'))
where = atoi(p+1);
}
/* uppercase search string, remove pads, and store fwd/rev copies */
patlen = strlen(value);
depad_seq(value, &patlen, NULL);
if (NULL == (uppert = (char *)xmalloc(patlen + 1)))
return 0;
if (NULL == (upperb = (char *)xmalloc(patlen + 1)))
return 0;
uppert[patlen] = upperb[patlen] = 0;
for (i = patlen-1; i >= 0; i--) {
upperb[i] = uppert[i] = toupper(value[i]);
}
complement_seq(upperb, patlen);
while ((r = ifunc(xx->io, iter))) {
seq_t *s, *sorig;
char *ind, *indt = NULL, *indb = NULL, *seq;
int seq_len, comp, off = 0;
if (found && dir && r->start > best_pos)
break;
if (found && !dir && r->end < best_pos)
break;
if (NULL == (s = sorig = cache_search(xx->io, GT_Seq, r->rec)))
break;
if (r->comp ^ (s->len < 0)) {
s = dup_seq(s);
complement_seq_t(s);
}
seq = s->seq;
seq_len = ABS(s->len);
if (r->start < start) {
off = start - r->start;
seq += off;
seq_len -= off;
}
if (r->end - (patlen-1) > end)
seq_len -= r->end - (patlen-1) - end;
if (dir) {
if (strand == '+' || strand == '=')
indt = pstrnstr_inexact(seq, seq_len, uppert, patlen,
mismatches, NULL);
if (strand == '-' || strand == '=')
indb = pstrnstr_inexact(seq, seq_len, upperb, patlen,
mismatches, NULL);
} else {
if (strand == '+' || strand == '=')
indt = prstrnstr_inexact(seq, seq_len, uppert, patlen,
mismatches, NULL);
if (strand == '-' || strand == '=')
indb = prstrnstr_inexact(seq, seq_len, upperb, patlen,
mismatches, NULL);
}
if (indt && indb)
ind = MIN(indt, indb);
else if (indt)
ind = indt;
else if (indb)
ind = indb;
else
ind = NULL;
if (ind) {
int pos = r->start + ind - seq + off;
if (dir) {
if (best_pos > pos) {
found = 1;
best_pos = pos;
fpos = ind - s->seq;
fseq = r->rec;
}
} else {
if (best_pos < pos) {
found = 1;
best_pos = pos;
fpos = ind - s->seq;
fseq = r->rec;
}
}
//printf("Matches #%"PRIrec": at abs pos %d\n", r->rec, pos);
}
if (s != sorig)
free(s);
}
if (found) {
edSetCursorPos(xx, fseq == xx->cnum ? GT_Contig : GT_Seq,
fseq, fpos, 1);
}
free(uppert);
free(upperb);
contig_iter_del(iter);
return found ? 0 : -1;
}
/*
* Checks a single reading for correct assembly by analysing the used data.
*
* Returns -1 for system error, otherwise a score (0-1000000)
* 'pos_p' and 'len_p' are filled in with the position and length of the match
* within the consensus.
*/
int check_uassembly_single(GapIO *io, char *cons, int contig, rangec_t *r,
float maxperc, int win_len, int ignore_N) {
int start, end;
unsigned char *seq = NULL;
unsigned char *con = (unsigned char *) cons;
int i, j, mism = 0;
int worst, worst_pos = -1;
seq_t *s, *sorig;
static int lookup[256];
static int lookup_done = 0;
if (!lookup_done) {
for (i = 0; i < 256; i++)
lookup[i] = 0;
lookup['A'] = lookup['a'] = 1;
lookup['C'] = lookup['c'] = 2;
lookup['G'] = lookup['g'] = 3;
lookup['T'] = lookup['t'] = 4;
lookup['U'] = lookup['u'] = 4;
lookup['*'] = lookup[','] = lookup['-'] = 5;
lookup_done = 1;
}
/* Get sequence */
if (!(sorig = s = cache_search(io, GT_Seq, r->rec)))
return -1;
/* Complement data on-the-fly */
if ((s->len < 0) ^ r->comp) {
s = dup_seq(s);
complement_seq_t(s);
}
seq = (unsigned char *) s->seq;
start = s->left;
end = s->right;
/* Initialise scoring for divergence checks */
if (end - start - 1 < win_len) {
win_len = end - start - 1;
}
worst = 0.5 + maxperc * win_len;
for (i=start-1, j=r->start + start-1; i < start-1 + win_len; i++, j++) {
if (ignore_N) {
if (lookup[seq[i]] && lookup[seq[i]] != lookup[con[j]])
mism++;
} else {
if (lookup[seq[i]] != lookup[con[j]])
mism++;
}
}
/* Loop through sequence looking for problems */
if (ignore_N) {
do {
if (mism >= worst) {
worst_pos = i;
worst = mism;
}
mism -= lookup[seq[i-win_len]] &&
lookup[seq[i-win_len]] != lookup[con[j-win_len]];
i++; j++;
if (i < end-1)
mism += lookup[seq[i]] && lookup[seq[i]] != lookup[con[j]];
} while (i < end);
} else {
do {
if (mism >= worst) {
worst_pos = i;
worst = mism;
}
mism -= lookup[seq[i++-win_len]] != lookup[con[j++-win_len]];
if (i < end-1)
mism += lookup[seq[i]] != lookup[con[j]];
} while (i < end);
}
/* Display problem, listing worst score */
if (worst_pos != -1) {
//*pos_p = io_relpos(io, rn);
//*len_p = end - start + 1;
vmessage("\nReading #%"PRIrec"(%s) has a local percentage "
"mismatch of %2.1f\n",
s->rec, s->name, 100 * (float)worst / win_len);
vmessage("SEQ: %.*s\n", end-start+1, &seq[start-1]);
vmessage("CON: %.*s\n", end-start+1, &con[r->start + start-1]);
if (sorig != s)
xfree(s);
return 10000 * (float)worst / win_len;
}
if (sorig != s)
xfree(s);
return 0;
}
/**
* 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);
}
/*
* Takes a multiple alignment and updates the on-disk data structures to
* match. This needs to correct confidence values, original positions and
* tags too.
*/
void update_io(GapIO *io, tg_rec cnum, MALIGN *malign, Array indels) {
CONTIGL *cl;
tg_rec rnum;
range_t r, *r_out;
bin_index_t *bin;
contig_t *c = cache_search(io, GT_Contig, cnum);
size_t i, nindel;
cache_incr(io, c);
/*
* To minimise number of data modifications we use a three step approach.
*
* Step 1: insert columns of pads, shifting reads as appropriate.
* Step 2: edit sequence alignments as required, possibly involving
* moving sequences and/or adding and removing pads.
* Step 3: remove columns of entire pads.
*
* This means that when we introduce a column of pads we don't have
* to make edits to every single read position down stream, and can
* instead make use of the optimised recursive bin functions to do this
* for us.
*/
/* Step 1: make indels */
nindel = ArrayMax(indels);
for (i = 0; i < nindel; i++) {
con_indel_t *id = arrp(con_indel_t, indels, i);
int j;
if (id->size > 0) {
contig_insert_bases(io, &c, id->pos+1, '*', -1, id->size);
} else {
for (j = 0; j < -id->size; j++) {
contig_delete_pad(io, &c, id->pos+1);
}
}
}
/* Step 2: edit alignments */
for (cl = malign->contigl; cl; cl = cl->next) {
seq_t *s, *sorig;
int len, update_range = 0;
int shift;
rnum = cl->id;
sorig = cache_search(io, GT_Seq, rnum);
cache_incr(io, sorig);
s = dup_seq(sorig);
if (cl->mseg->comp)
complement_seq_t(s);
len = s->right - s->left + 1;
/* Check if sequence has changed. If so assign a new one */
if (cl->mseg->length != len ||
memcmp(s->seq + s->left-1, cl->mseg->seq, cl->mseg->length) != 0) {
int newlen = s->left-1 + ABS(s->len) - s->right + cl->mseg->length;
int i, j, np;
char *newseq = malloc(newlen+1);
int8_t *newconf = malloc(newlen+1);
/* Build new seq/conf arrays */
memcpy(newseq, s->seq, s->left-1);
memcpy(newconf, s->conf, s->left-1);
memcpy(&newseq[s->left-1], cl->mseg->seq, cl->mseg->length);
/*
* Step through both old and new sequences working out how
* they differ. This will (*should*) be entire pad movements.
* i = index to old seq
* j = index to new seq
* np = number of pads added minus removed from old seq.
*/
np = 0;
for (i =j =s->left-1;
i < ABS(s->len) && j < s->left-1 + cl->mseg->length;
) {
/* Bases match */
if (toupper(newseq[j]) == toupper(s->seq[i]) ||
(s->seq[i] == '.' && newseq[j] == 'N')) {
if (isupper(s->seq[i]))
newseq[j] = toupper(newseq[j]);
else
newseq[j] = tolower(newseq[j]);
newconf[j] = s->conf[i];
i++, j++;
continue;
}
/* Pad removed */
if (s->seq[i] == '*') {
i++;
tag_shift_for_delete(io, cnum, rnum, cl->mseg->offset,
cl->mseg->length, i+np--,
s->bin);
/*
if (io_length(io, rnum) < 0) {
tag_shift_for_delete(io, rnum, r.length - i + 1);
} else {
tag_shift_for_delete(io, rnum, i+np--);
}
*/
continue;
}
/* Pad created */
if (newseq[j] == '*') {
int k;
int ql = 0, qr = 0;
for (k = i-1; k >= 0; k--) {
if (s->seq[k] != '*') {
ql = s->conf[k];
break;
}
}
for (k = i+1; k < s->right; k++) {
if (s->seq[k] != '*') {
qr = s->conf[k];
break;
}
}
newconf[j] = MIN(ql, qr); /* min conf of neighbours */
j++;
tag_shift_for_insert(io, cnum, rnum, cl->mseg->offset,
cl->mseg->length, i+ ++np,
s->bin);
/*
if (io_length(io, rnum) < 0) {
tag_shift_for_insert(io, rnum, r.length - i + 1);
} else {
tag_shift_for_insert(io, rnum, i+ ++np);
}
*/
continue;
}
fprintf(stderr, "Alignment introduced non-pad character");
abort();
}
/* Pads previously at the end of the reading & now removed */
while (i < s->right) {
if (s->seq[i] == '*') {
i++;
tag_shift_for_delete(io, cnum, rnum, cl->mseg->offset,
cl->mseg->length, i+np--,
s->bin);
/*
if (io_length(io, rnum) < 0) {
tag_shift_for_delete(io, rnum, r.length - i + 1);
} else {
tag_shift_for_delete(io, rnum, i+np--);
}
*/
} else {
/* Error: clipped data that wasn't a pad */
abort();
}
}
/* Should only be pads remaining in newseq, if anything */
s->right = j;
for (; j < s->left-1 + cl->mseg->length; j++) {
if (newseq[j] != '*') {
fprintf(stderr, "Alignment introduced non-pad character");
abort();
}
newconf[j] = 0;
}
/* Append on the right hand cutoff data */
for (; i < ABS(s->len); i++, j++) {
newseq[j] = s->seq[i];
newconf[j] = s->conf[i];
}
if (j != newlen) {
abort();
}
/* Write it back out */
/* Copy newseq/newconf into seq_t */
s->seq = newseq;
s->conf = newconf;
update_range = 0;
if (ABS(s->len) != j) {
/* Length change implies updating the range array too */
s->len = s->len >= 0 ? j : -j;
update_range = 1;
}
if (cl->mseg->comp)
complement_seq_t(s);
/* The memcpy trashes the block pointer, so special care needed */
{
sorig = cache_rw(io, sorig);
void *blk = sorig->block;
memcpy(sorig, s, sizeof(seq_t));
sorig->block = blk;
}
if (update_range)
sorig = cache_item_resize(sorig, sizeof(*sorig) +
sequence_extra_len(sorig));
sequence_reset_ptr(sorig);
if (s->name)
memcpy(sorig->name, s->name, s->name_len+1);
if (s->trace_name)
memcpy(sorig->trace_name, s->trace_name, s->trace_name_len+1);
if (s->alignment)
memcpy(sorig->alignment, s->alignment, s->alignment_len+1);
memcpy(sorig->seq, s->seq, ABS(s->len));
memcpy(sorig->conf, s->conf, ABS(s->len));
xfree(newconf);
xfree(newseq);
}
{
int st, en, or;
sequence_get_position(io, s->rec, NULL, &st, &en, &or);
if (or ^ (sorig->len < 0)) {
shift = ABS(sorig->len) - sorig->right;
} else {
shift = sorig->left-1;
}
st += shift;
if (st != cl->mseg->offset+1) {
update_range = 1;
}
}
free(s);
if (update_range) {
int bin_changed = 0;
/* Get old range and pair data */
s = sorig;
bin = cache_search(io, GT_Bin, s->bin);
r = *arrp(range_t, bin->rng, s->bin_index);
assert(r.rec == s->rec);
/* Update range, tedious and slow way */
bin_remove_item(io, &c, GT_Seq, s->rec);
r.start = cl->mseg->offset + 1 - shift;
r.end = r.start + ABS(s->len) - 1;
bin = bin_add_range(io, &c, &r, &r_out, NULL, 0);
/* Check if the new bin has a different complemented status too */
if (s->bin != bin->rec) {
int old_comp = bin_get_orient(io, s->bin);
int new_comp = bin_get_orient(io, bin->rec);
if (new_comp != old_comp) {
//int tmp;
s = cache_rw(io, s);
s->len *= -1;
s->flags ^= SEQ_COMPLEMENTED;
//tmp = s->left;
//s->left = ABS(s->len) - (s->right-1);
//s->right = ABS(s->len) - (tmp-1);
}
bin_changed = 1;
}
/* Update seq bin & bin_index fields */
s = cache_rw(io, s);
s->bin = bin->rec;
s->bin_index = r_out - ArrayBase(range_t, bin->rng);
if (bin_changed) {
if (-1 == sequence_fix_anno_bins(io, &s)) {
verror(ERR_WARN, "update_io",
"sequence_fix_anno_bins() failure");
}
}
}
cache_decr(io, sorig);
}
/* Step 3 (remove pad columns) done in calling function. */
cache_decr(io, c);
}
/*
* Compute a basic non-weighted consensus. We simply pick the basecall
* most frequently used.
*
* FIXME: use a weighted sum based on confidence values instead?
*/
int calc_cons(GapIO *io, rangec_t *r, int nr, int xpos, int wid,
char *cons) {
int i, j;
int (*cvec)[6] = (int (*)[6])calloc(wid, 6 * sizeof(int));
if (!lookup_done) {
memset(lookup, 5, 256);
lookup_done = 1;
lookup['A'] = lookup['a'] = 0;
lookup['C'] = lookup['c'] = 1;
lookup['G'] = lookup['g'] = 2;
lookup['T'] = lookup['t'] = 3;
lookup['*'] = lookup[','] = 4;
}
/* Accumulate */
for (i = 0; i < nr; i++) {
int sp = r[i].start;
seq_t *s = get_seq(io, r[i].rec);
seq_t *sorig = s;
int l = s->len > 0 ? s->len : -s->len;
unsigned char *seq;
int left, right;
/* Complement data on-the-fly */
if ((s->len < 0) ^ r[i].comp) {
s = dup_seq(s);
complement_seq_t(s);
}
seq = (unsigned char *)s->seq;
left = s->left;
right = s->right;
if (sp < xpos) {
seq += xpos - sp;
l -= xpos - sp;
left -= xpos - sp;
right -= xpos - sp;
sp = xpos;
}
if (l > wid - (sp-xpos))
l = wid - (sp-xpos);
if (left < 1)
left = 1;
for (j = left-1; j < right; j++) {
if (sp-xpos+j < wid)
cvec[sp-xpos+j][lookup[seq[j]]]++;
}
if (s != sorig)
free(s);
}
memset(cons, ' ', wid);
/* and speculate :-) */
for (i = 0; i < wid; i++) {
int max, max_base = 5;
for (max = j = 0; j < 6; j++) {
if (max < cvec[i][j]) {
max = cvec[i][j];
max_base = j;
}
}
cons[i] = "ACGT*N"[max_base];
}
free(cvec);
return 0;
}
static void display_gap(GapIO *io, contig_t **c, int xpos, int ypos,
int nlines, int wid, int mode, int qual_cutoff,
int in_curses) {
rangec_t *r;
int i, nr, lno, y;
char line[1024], *lp;
char cons[1024];
int attr;
static int lookup_1conf[256];
static int lookup_4conf[256];
static int lookup_init = 0;
if (!lookup_init) {
for (i = 0; i < 256; i++)
lookup_1conf[i] = lookup_4conf[0] = 0;
lookup_4conf['a'] = lookup_4conf['A'] = 0;
lookup_4conf['c'] = lookup_4conf['C'] = 1;
lookup_4conf['g'] = lookup_4conf['G'] = 2;
lookup_4conf['t'] = lookup_4conf['T'] = 3;
}
wid -= MAX_NAME_LEN+2;
//if (xpos < wid/2 + (*c)->start)
// xpos = wid/2 + (*c)->start;
xpos -= wid/2;
/* Query visible objects */
r = contig_seqs_in_range(io, c, xpos, xpos+wid-1, CSIR_SORT_BY_X, &nr);
/* Consensus */
calc_cons(io, r, nr, xpos, wid, cons);
if (in_curses) {
clear();
mvaddnstr(0, 1, contig_get_name(c), strlen(contig_get_name(c)));
mvaddnstr(0, MAX_NAME_LEN+2, cons, wid);
} else {
printf(" %-*s %.*s\n", MAX_NAME_LEN, contig_get_name(c), wid, cons);
}
/* Position */
for (lp = line, i = xpos; i < xpos+wid+19; i++) {
if (i % 10 == 0) {
sprintf(lp, "%10d", i-10);
lp += 10;
}
}
if (in_curses) {
int m = (xpos-1)%10;
if (m < 0) m += 10;
mvaddnstr(1, MAX_NAME_LEN+2, line+10+m, wid);
} else {
printf("%*s%.*s\n", MAX_NAME_LEN+2, "", wid,
line+9+((xpos-1)%10));
}
/* Sequences */
for (i = y = 0; i < nr && y < ypos; i++, y++);
for (lno = 2; i < nr && lno < nlines; i++, lno++) {
seq_t *s = get_seq(io, r[i].rec);
seq_t *sorig = s;
int sp = r[i].start;
int l = s->len > 0 ? s->len : -s->len;
unsigned char seq_a[MAX_SEQ_LEN], *seq = seq_a;
int j, dir = '+';
int left, right;
char *conf;
int nc = s->format == SEQ_FORMAT_CNF4 ? 4 : 1;
int *L = s->format == SEQ_FORMAT_CNF4 ? lookup_4conf : lookup_1conf;
/* Complement data on-the-fly */
if ((s->len < 0) ^ r[i].comp) {
dir = '-';
s = dup_seq(s);
complement_seq_t(s);
}
left = s->left;
right = s->right;
memcpy(seq, s->seq, l);
conf = s->conf;
if (sp < xpos) {
seq += xpos - sp;
conf += nc * (xpos - sp);
l -= xpos - sp;
left -= xpos - sp;
right -= xpos - sp;
sp = xpos;
}
if (l > wid - (sp-xpos))
l = wid - (sp-xpos);
if (in_curses) {
/* Test of sequence_get_position */
/*
int c, p;
sequence_get_position(io, r[i].rec, &c, &p);
s->name_len = sprintf(s->name, ":%d-%d:", p, p+ABS(s->len)-1);
*/
mvaddch(lno, 0, dir);
addnstr(s->name, MIN(MAX_NAME_LEN, s->name_len));
move(lno, MAX_NAME_LEN+2+sp-xpos);
} else {
printf("%c%.*s%*s",
dir,
MIN(MAX_NAME_LEN, s->name_len), s->name,
MAX_NAME_LEN+1-MIN(MAX_NAME_LEN, s->name_len) +sp-xpos, "");
}
for (j = 0; j < l; j++) {
attr = (mode & DISPLAY_COLOURS) ? COLOR_PAIR(lookup[seq[j]]) : 0;
if (mode & DISPLAY_DIFFS
&& sp-xpos+j < wid && seq[j] == cons[sp-xpos+j])
seq[j] = '.';
if (j < left-1 || j > right-1)
seq[j] = (mode & DISPLAY_CUTOFFS) ? tolower(seq[j]) : ' ';
if (conf[j*nc+L[seq[j]]] >= qual_cutoff && mode & DISPLAY_QUAL) {
attr |= A_BOLD;
}
if (in_curses) {
addch(seq[j] | attr);
} else {
putchar(seq[j]);
}
}
if (!in_curses)
putchar('\n');
if (s != sorig)
free(s);
}
/* Useful debugging code to show bin locations. */
#if 0
free(r);
r = contig_bins_in_range(io, c, xpos, xpos+wid-1, &nr);
/* Bins */
for (i=0; i < nr && lno < nlines; i++, lno++) {
bin_index_t *bin = (bin_index_t *)cache_search(io, GT_Bin, r[i].rec);
unsigned char *seq, *seqm;
int j, dir = "+-"[r[i].comp];
int sp = r[i].start;
int l = ABS(r[i].end - r[i].start + 1);
char name[100];
sprintf(name, "bin-%d", bin->rec);
seqm = seq = malloc(l+1);
memset(seq, '-', l);
if (!(bin->start_used == 0 && bin->end_used == 0)) {
if (r[i].comp) {
memset(&seq[bin->size - bin->end_used - 1], '=',
bin->end_used - bin->start_used + 1);
} else {
memset(&seq[bin->start_used], '=',
bin->end_used - bin->start_used + 1);
}
}
/*
fprintf(stderr, "Bin-%d: %d+%d %d..%d\n",
bin->rec,
bin->pos, bin->size,
bin->start_used, bin->end_used);
*/
if (sp < xpos) {
seq += xpos - sp;
l -= xpos - sp;
sp = xpos;
}
if (l > wid - (sp-xpos))
l = wid - (sp-xpos);
if (in_curses) {
mvaddch(lno, 0, dir);
addnstr(name, strlen(name));
move(lno, MAX_NAME_LEN+2+sp-xpos);
} else {
printf("%c%.*s%*s",
dir,
(int)MIN(MAX_NAME_LEN, strlen(name)),
name,
(int)(MAX_NAME_LEN+1-MIN(MAX_NAME_LEN,
strlen(name)) +sp-xpos),
"");
}
for (j = 0; j < l; j++) {
if (in_curses) {
addch(seq[j]);
} else {
putchar(seq[j]);
}
}
if (!in_curses)
putchar('\n');
free(seqm);
}
#endif
if (in_curses)
refresh();
free(r);
}
/*
* Extends the right hand end of a single contig.
*
* Min_depth is the minimum depth for extension. If lower then even if the
* data matches we'll not extend further.
*
* Match_score (+ve) and mismatch_score (-ve) are accumulated during
* extension to ensure that we don't extend into junk mismatching DNA.
*/
static int contig_extend_single(GapIO *io, tg_rec crec, int dir, int min_depth,
int match_score, int mismatch_score) {
int end;
rangec_t *r;
int nr, i;
contig_t *c;
char cons[CSZ], new_cons[ESZ];
int freqs[ESZ][4], depth[ESZ];
double score, best_score;
int best_pos, nseq;
vmessage("Processing contig #%"PRIrec", %s end\n",
crec, dir ? "left" : "right");
for (i = 0; i < ESZ; i++) {
freqs[i][0] = freqs[i][1] = freqs[i][2] = freqs[i][3] = 0;
depth[i] = 0;
}
c = cache_search(io, GT_Contig, crec);
if (NULL == c) return -1;
cache_incr(io, c);
if (consensus_valid_range(io, crec, NULL, &end) != 0) {
cache_decr(io, c);
return -1;
}
calculate_consensus_simple(io, crec, end-(CSZ-1), end, cons, NULL);
/* Start */
/* Not implemented for now: rev complement and go again! */
/* End */
r = contig_seqs_in_range(io, &c, end, end, 0, &nr);
if (!r) {
cache_decr(io, c);
return -1;
}
for (i = 0; i < nr; i++) {
seq_t *s = cache_search(io, GT_Seq, r[i].rec);
seq_t *sorig = s;
int cstart, cend;
int j, k, slen;
if ((s->len < 0) ^ r[i].comp) {
s = dup_seq(s);
complement_seq_t(s);
}
cstart = r[i].start + s->left-1;
cend = r[i].start + s->right-1;
/* Does cutoff extend to contig end, if so does it match cons? */
if (cend < end) {
int mis = 0, len = 0;
if (end - cend >= CSZ) {
/*
fprintf(stderr,"Skipping #%"PRIrec" due to length of cutoff\n",
r[i].rec);
*/
if (sorig != s)
free(s);
r[i].rec = 0; /* Mark for removal */
continue;
}
for (k = s->right, j = cend+1; j <= end; j++, k++) {
//printf("%d: %c %c\n", j, s->seq[k], cons[j-(end-(CSZ-1))]);
if (s->seq[k] != cons[j-(end-(CSZ-1))])
mis++;
}
len = end - cend;
if (100*mis/len > 5) {
/*
fprintf(stderr, "Skipping #%"PRIrec" due to high disagreement "
"with consensus.\n", r[i].rec);
*/
if (sorig != s)
free(s);
r[i].rec = 0;
continue;
}
}
/* So we got here, let's accumulate extension stats */
slen = ABS(s->len);
for (k = 0, j = end+1 - r[i].start; j < slen && k < ESZ; j++, k++) {
//printf("%d: %c\n", j + r[i].start, s->seq[j]);
if(s->seq[j] == 'N')
continue;
freqs[k][dna_lookup[(uint8_t) s->seq[j]]]++;
depth[k]++;
}
if (sorig != s)
free(s);
}
score = best_score = 0;
best_pos = 0;
for (i = 0; i < ESZ; i++) {
int call, best = 0, j;
double dd;
if (depth[i] < min_depth)
break;
for (j = 0; j < 4; j++) {
if (best < freqs[i][j]) {
best = freqs[i][j];
call = j;
}
}
new_cons[i] = "ACGT"[call];
dd = (double)depth[i];
switch (call) {
case 0:
score += freqs[i][0] / dd;
score -= (freqs[i][1] + freqs[i][2] + freqs[i][3]) / dd;
break;
case 1:
score += freqs[i][1] / dd;
score -= (freqs[i][0] + freqs[i][2] + freqs[i][3]) / dd;
break;
case 2:
score += freqs[i][2] / dd;
score -= (freqs[i][0] + freqs[i][1] + freqs[i][3]) / dd;
break;
case 3:
score += freqs[i][3] / dd;
score -= (freqs[i][0] + freqs[i][1] + freqs[i][2]) / dd;
break;
}
if (best_score <= score) {
best_score = score;
best_pos = i+1;
}
/*
printf("%3d %3d\t%c\t%3d %3d %3d %3d %7.1f\n",
i, depth[i], "ACGT"[call],
freqs[i][0], freqs[i][1], freqs[i][2], freqs[i][3],
score);
*/
}
/* printf("Best score is %f at %d\n", best_score, best_pos); */
/* Extend */
nseq = 0;
if (best_pos > 0) {
int furthest_left = end;
for (i = 0; i < nr; i++) {
seq_t *s;
int r_pos;
int score;
if (r[i].rec == 0)
continue;
s = cache_search(io, GT_Seq, r[i].rec);
s = cache_rw(io, s);
if (furthest_left > r[i].start)
furthest_left = r[i].start;
/*
* end + best_pos is the furthest right we can go, but this
* specific read may not be justified in reaching that far
* if it has too many disagreements.
*/
if ((s->len > 0) ^ r[i].comp) {
int best_r = 0, j, k;
int len = ABS(s->len);
//printf(">%s\t", s->name);
r_pos = 0;
score = 0;
//for (k = s->right, j = 0; j < best_pos && k < len; j++, k++) {
for (k = end - r[i].start + 1, j = 0; j < best_pos && k < len; j++, k++) {
if (new_cons[j] == toupper(s->seq[k])) {
score += match_score;
if (best_r <= score) {
best_r = score;
r_pos = k+1;
}
} else {
score += mismatch_score;
}
//putchar(new_cons[j] == toupper(s->seq[k])
// ? toupper(s->seq[k])
// : tolower(s->seq[k]));
}
//putchar('\n');
if (s->right != r_pos) {
s->right = r_pos;
nseq++;
}
} else {
int best_r = 0, j, k;
//printf("<%s\t", s->name);
r_pos = 0;
score = 0;
//for (k = s->left-2, j = 0; j < best_pos && k >= 0; j++, k--) {
for (k = r[i].end - end - 1, j = 0; j < best_pos && k >= 0; j++, k--) {
char b = complement_base(s->seq[k]);
if (new_cons[j] == b) {
score += match_score;
if (best_r <= score) {
best_r = score;
r_pos = k-1;
}
} else {
score += mismatch_score;
}
//putchar(new_cons[j] == toupper(b)
// ? toupper(b)
// : tolower(b));
}
//putchar('\n');
if (s->left != r_pos+2) {
s->left = r_pos+2;
nseq++;
}
}
}
vmessage(" Extended by %d, adjusting %d sequence clip%s\n",
best_pos, nseq, nseq == 1 ? "" : "s");
bin_invalidate_consensus(io, crec, furthest_left, end + best_pos);
} else {
vmessage(" Unable to extend contig\n");
}
free(r);
cache_decr(io, c);
cache_flush(io);
return 0;
}
