DnaNumber dna_number_from_string(char * str,int nmer_size)
{
int i;
int base = 1;
DnaNumber out;
int forward;
int backward;
out.flipped = 2;
out.number = 0;
for(i=0;i<nmer_size-1;i++)
base *= 4;
for(i=0;i<nmer_size;i++) {
forward = base_from_char(str[i]);
backward = complement_base(base_from_char(str[nmer_size-1-i]));
if( forward == BASE_N || backward == BASE_N ) {
return out;
}
if( forward > backward ) {
out.flipped = 0;
break;
}
if( backward > forward ) {
out.flipped = 1;
break;
}
}
assert(out.flipped != 2);
if( out.flipped == 0 ) {
for(i=0;i<nmer_size;i++) {
out.number += base * base_from_char(str[i]);
base = base / 4;
}
} else {
for(i=0;i<nmer_size;i++) {
/* fprintf(stderr,"For position %d, [%d], using %d [%c]as complemented base\n",i,base,complement_base(base_from_char(str[nmer_size-1-i])),str[nmer_size-1-i]); */
out.number += base * complement_base(base_from_char(str[nmer_size-1-i]));
base = base / 4;
}
}
return out;
}
pairbase_type complement_pairbase(pairbase_type b)
{
pairbase_type anchor;
pairbase_type informant;
anchor = anchor_base_from_pairbase(b);
informant = informant_base_from_pairbase(b);
/* we reverse completement anchor */
anchor = complement_base(anchor);
if( informant != BASE_GAP && informant != BASE_OPEN ) {
informant = complement_base(informant);
}
return MAKE_PAIRBASE(anchor,informant);
}
char first_char_from_dnanumber(int dnanumber,int nmer_size,int flipped)
{
int base = 1;
int basepair;
int power;
int i;
if( flipped == 1 ) {
/* first number is therefore lowest bit */
basepair = dnanumber % 4;
/* fprintf(stderr,"Going to use %d as number\n",basepair);*/
basepair = complement_base(basepair);
return char_from_base(basepair);
} else {
for(i=0;i<nmer_size-1;i++)
base *= 4;
basepair = (int) (dnanumber / base);
return char_from_base(basepair);
}
}
char char_complement_base(char c)
{
return char_from_base(complement_base(base_from_char(c)));
}
/*
* 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;
}
