/* 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);
}
static void benchmark(GapIO *io, contig_t **c) {
int i;
char cons[10000];
srandom(0);
fprintf(stderr, "=== Benchmarking ===\n");
for (i = 0; i < 1000; i++) {
int xpos = random() % 2000000;
int size = random() % 1000;
int nr;
rangec_t *r;
r = contig_seqs_in_range(io, c, xpos, xpos+size, 0, &nr);
calc_cons(io, r, nr, xpos, size, cons);
printf("%.*s\n", size, cons);
fputc('.', stderr);
fflush(stderr);
free(r);
}
gio_close(io);
exit(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;
}
