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r444: changed the way orientation is specified

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The old model doesn't work with RF or RR orientation. The new model only works
with paired-end reads. For >2 segments, only FF is supported.
This commit is contained in:
Heng Li
2017-09-27 12:33:10 -04:00
parent f611edf6f2
commit a349d85280
4 changed files with 39 additions and 13 deletions
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map.c
+8 -6
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@@ -12,7 +12,8 @@ void mm_mapopt_init(mm_mapopt_t *opt)
{
memset(opt, 0, sizeof(mm_mapopt_t));
opt->mid_occ_frac = 2e-4f;
opt->sdust_thres = 0;
opt->sdust_thres = 0; // no SDUST masking
opt->pe_ori = 0; // FF
opt->min_cnt = 3;
opt->min_chain_score = 40;
@@ -75,7 +76,8 @@ int mm_set_opt(const char *preset, mm_idxopt_t *io, mm_mapopt_t *mo)
mo->min_dp_max = 200;
} else if (strcmp(preset, "short") == 0 || strcmp(preset, "sr") == 0) {
io->is_hpc = 0, io->k = 21, io->w = 11;
mo->flag |= MM_F_SR | MM_F_MULTI_SEG | MM_F_SEG_REV;
mo->flag |= MM_F_SR | MM_F_MULTI_SEG;
mo->pe_ori = 0<<1|1; // FR
mo->a = 2, mo->b = 8, mo->q = 12, mo->e = 2, mo->q2 = 32, mo->e2 = 1;
mo->max_gap = 200;
mo->max_gap_ref = 1000;
@@ -339,7 +341,7 @@ typedef struct {
static void worker_for(void *_data, long i, int tid) // kt_for() callback
{
step_t *s = (step_t*)_data;
int *qlens, j, off = s->seg_off[i];
int *qlens, j, off = s->seg_off[i], pe_ori = s->p->opt->pe_ori;
const char **qseqs;
mm_tbuf_t *b = s->buf[tid];
if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
@@ -347,14 +349,14 @@ static void worker_for(void *_data, long i, int tid) // kt_for() callback
qlens = (int*)kmalloc(b->km, s->n_seg[i] * sizeof(int));
qseqs = (const char**)kmalloc(b->km, s->n_seg[i] * sizeof(const char**));
for (j = 0; j < s->n_seg[i]; ++j) {
if (j > 0 && (s->p->opt->flag & MM_F_SEG_REV))
if (s->n_seg[i] == 2 && ((j == 0 && (pe_ori>>1&1)) || (j == 1 && (pe_ori&1))))
mm_revcomp_bseq(&s->seq[off + j]);
qlens[j] = s->seq[off + j].l_seq;
qseqs[j] = s->seq[off + j].seq;
}
mm_map_multi(s->p->mi, s->n_seg[i], qlens, qseqs, &s->n_reg[off], &s->reg[off], b, s->p->opt, s->seq[off].name);
if (s->n_seg[i] > 1 && (s->p->opt->flag & MM_F_SEG_REV))
for (j = 1; j < s->n_seg[i]; ++j) { // flip the query strand and coordinate to the original read strand
for (j = 0; j < s->n_seg[i]; ++j) // flip the query strand and coordinate to the original read strand
if (s->n_seg[i] == 2 && ((j == 0 && (pe_ori>>1&1)) || (j == 1 && (pe_ori&1)))) {
int k, t;
mm_revcomp_bseq(&s->seq[off + j]);
for (k = 0; k < s->n_reg[off + j]; ++k) {