fork/minimap2
1
0
Fork 0
mirror of https://github.com/lh3/minimap2.git synced 2026-10-02 07:38:12 +08:00
Code Issues Packages Projects Releases Wiki Activity

r477: renamed multi_seg to frag_mode

Browse Source
This commit is contained in:
Heng Li
2017-10-05 15:48:17 -04:00
parent ae2adf04d4
commit 9c5767f9ed
5 changed files with 25 additions and 24 deletions
Download Patch File Download Diff File Expand all files Collapse all files
map.c
+10 -10
View File
@@ -80,7 +80,7 @@ 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_NO_PRINT_2ND;
mo->flag |= MM_F_SR | MM_F_FRAG_MODE | MM_F_NO_PRINT_2ND;
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;
@@ -261,7 +261,7 @@ static mm_reg1_t *align_regs(const mm_mapopt_t *opt, const mm_idx_t *mi, void *k
return regs;
}
void mm_map_multi(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
{
int i, j, max_gap_ref, rep_len, qlen_sum, n_regs0, rechain = 0;
uint32_t hash;
@@ -350,7 +350,7 @@ void mm_map_multi(const mm_idx_t *mi, int n_segs, const int *qlens, const char *
mm_reg1_t *mm_map(const mm_idx_t *mi, int qlen, const char *seq, int *n_regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
{
mm_reg1_t *regs;
mm_map_multi(mi, 1, &qlen, &seq, n_regs, &regs, b, opt, qname);
mm_map_frag(mi, 1, &qlen, &seq, n_regs, &regs, b, opt, qname);
return regs;
}
@@ -391,7 +391,7 @@ static void worker_for(void *_data, long i, int tid) // kt_for() callback
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);
mm_map_frag(s->p->mi, s->n_seg[i], qlens, qseqs, &s->n_reg[off], &s->reg[off], b, s->p->opt, s->seq[off].name);
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;
@@ -414,11 +414,11 @@ static void *worker_pipeline(void *shared, int step, void *in)
pipeline_t *p = (pipeline_t*)shared;
if (step == 0) { // step 0: read sequences
int with_qual = (!!(p->opt->flag & MM_F_OUT_SAM) && !(p->opt->flag & MM_F_NO_QUAL));
int multi_seg = (p->n_fp > 1 || !!(p->opt->flag & MM_F_MULTI_SEG));
int frag_mode = (p->n_fp > 1 || !!(p->opt->flag & MM_F_FRAG_MODE));
step_t *s;
s = (step_t*)calloc(1, sizeof(step_t));
if (p->n_fp > 1) s->seq = mm_bseq_read_multi(p->n_fp, p->fp, p->mini_batch_size, with_qual, &s->n_seq);
else s->seq = mm_bseq_read2(p->fp[0], p->mini_batch_size, with_qual, multi_seg, &s->n_seq);
if (p->n_fp > 1) s->seq = mm_bseq_read_frag(p->n_fp, p->fp, p->mini_batch_size, with_qual, &s->n_seq);
else s->seq = mm_bseq_read2(p->fp[0], p->mini_batch_size, with_qual, frag_mode, &s->n_seq);
if (s->seq) {
s->p = p;
for (i = 0; i < s->n_seq; ++i)
@@ -431,7 +431,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
s->n_seg = s->seg_off + s->n_seq;
s->reg = (mm_reg1_t**)calloc(s->n_seq, sizeof(mm_reg1_t*));
for (i = 1, j = 0; i <= s->n_seq; ++i)
if (i == s->n_seq || !multi_seg || !mm_qname_same(s->seq[i-1].name, s->seq[i].name)) {
if (i == s->n_seq || !frag_mode || !mm_qname_same(s->seq[i-1].name, s->seq[i].name)) {
s->n_seg[s->n_frag] = i - j;
s->seg_off[s->n_frag++] = j;
j = i;
@@ -484,7 +484,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
return 0;
}
int mm_map_file_multi_seg(const mm_idx_t *idx, int n_segs, const char **fn, const mm_mapopt_t *opt, int n_threads)
int mm_map_file_frag(const mm_idx_t *idx, int n_segs, const char **fn, const mm_mapopt_t *opt, int n_threads)
{
int i, j;
pipeline_t pl;
@@ -516,5 +516,5 @@ int mm_map_file_multi_seg(const mm_idx_t *idx, int n_segs, const char **fn, cons
int mm_map_file(const mm_idx_t *idx, const char *fn, const mm_mapopt_t *opt, int n_threads)
{
return mm_map_file_multi_seg(idx, 1, &fn, opt, n_threads);
return mm_map_file_frag(idx, 1, &fn, opt, n_threads);
}