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r273: cdna mapping mode for testing

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Differences from the typical mapping mode:

* banded alignment disabled
* log gap cost during chaining
* zero long-gap extension during alignment
* up to 100kb (by default) reference gap
* bad seeding not filtered (to tune later)
This commit is contained in:
Heng Li
2017-08-08 11:31:49 -04:00
parent 4badf2fcbf
commit 1a7d782131
6 changed files with 33 additions and 15 deletions
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chain.c
+9 -4
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@@ -19,7 +19,7 @@ static inline int ilog2_32(uint32_t v)
return (t = v>>8) ? 8 + LogTable256[t] : LogTable256[v];
}
int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int64_t n, mm128_t *a, uint64_t **_u, void *km)
int mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int min_cnt, int min_sc, int is_cdna, int64_t n, mm128_t *a, uint64_t **_u, void *km)
{ // TODO: make sure this works when n has more than 32 bits
int32_t st = 0, k, *f, *p, *t, *v, n_u, n_v;
int64_t i, j;
@@ -42,17 +42,22 @@ int mm_chain_dp(int max_dist, int bw, int max_skip, int min_cnt, int min_sc, int
uint64_t ri = a[i].x;
int32_t qi = (int32_t)a[i].y, q_span = a[i].y>>32&0xff; // NB: only 8 bits of span is used!!!
int32_t max_f = q_span, max_j = -1, n_skip = 0, min_d, max_f_past = -INT32_MAX;
while (st < i && ri - a[st].x > max_dist) ++st;
while (st < i && ri - a[st].x > max_dist_x) ++st;
for (j = i - 1; j >= st; --j) {
int64_t dr = ri - a[j].x;
int32_t dq = qi - (int32_t)a[j].y, dd, sc;
if (dr == 0 || dq <= 0 || dq > max_dist) continue;
if (dr == 0 || dq <= 0 || dq > max_dist_y) continue;
dd = dr > dq? dr - dq : dq - dr;
if (dd > bw) continue;
max_f_past = max_f_past > f[j]? max_f_past : f[j];
min_d = dq < dr? dq : dr;
sc = min_d > q_span? q_span : dq < dr? dq : dr;
sc -= (int)(dd * .01 * avg_qspan) + (ilog2_32(dd)>>1);
if (is_cdna) {
int c_log, c_lin;
c_lin = (int)(dd * .01 * avg_qspan);
c_log = ilog2_32(dd);
sc -= c_lin < c_log? c_lin : c_log;
} else sc -= (int)(dd * .01 * avg_qspan) + (ilog2_32(dd)>>1);
sc += f[j];
if (sc > max_f) {
max_f = sc, max_j = j;