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r170: added a debugging flag 

something wrong with chaining
This commit is contained in:
Heng Li 2017-07-11 14:47:35 -04:00
parent 801bc84b01
commit 826c8ba892
3 changed files with 10 additions and 3 deletions
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6
main.c
View File

@ -10,7 +10,7 @@
#include "minimap.h"
#include "mmpriv.h"
#define MM_VERSION "2.0-r169-pre"
#define MM_VERSION "2.0-r170-pre"
void liftrlimit()
{
@ -48,6 +48,7 @@ static struct option long_options[] = {
{ "no-kalloc", no_argument, 0, 0 },
{ "print-qname", no_argument, 0, 0 },
{ "no-self", no_argument, 0, 0 },
{ "print-seed", no_argument, 0, 0 },
{ "version", no_argument, 0, 'V' },
{ "min-count", required_argument, 0, 'n' },
{ "min-chain-score",required_argument, 0, 'm' },
@ -100,7 +101,8 @@ int main(int argc, char *argv[])
else if (c == 0 && long_idx == 2) keep_name = 0; // --int-rname
else if (c == 0 && long_idx == 3) mm_dbg_flag |= MM_DBG_NO_KALLOC; // --no-kalloc
else if (c == 0 && long_idx == 4) mm_dbg_flag |= MM_DBG_PRINT_QNAME; // --print-qname
else if (c == 0 && long_idx == 5) opt.flag |= MM_F_NO_SELF;
else if (c == 0 && long_idx == 5) opt.flag |= MM_F_NO_SELF; // --no-self
else if (c == 0 && long_idx == 6) mm_dbg_flag |= MM_DBG_PRINT_QNAME | MM_DBG_PRINT_SEED; // --print-seed
else if (c == 'V') {
puts(MM_VERSION);
return 0;

6
map.c
View File

@ -236,6 +236,10 @@ mm_reg1_t *mm_map_frag(const mm_mapopt_t *opt, const mm_idx_t *mi, mm_tbuf_t *b,
if (m[i].is_alloc) kfree(b->km, m[i].x.r);
kfree(b->km, m);
if (mm_dbg_flag & MM_DBG_PRINT_SEED)
for (i = 0; i < n_a; ++i)
fprintf(stderr, "SD\t%d\t%c\t%s\t%d\t%d\n", (int32_t)a[i].y, "+-"[a[i].x>>63], mi->seq[a[i].x<<1>>33].name, (int32_t)a[i].x, (int32_t)(a[i].y>>32&0xff));
n_u = mm_chain_dp(opt->max_gap, opt->bw, opt->max_chain_skip, opt->min_cnt, opt->min_chain_score, n_a, a, &u, b->km);
regs = mm_gen_regs(b->km, qlen, n_u, u, a);
*n_regs = n_u;
@ -296,7 +300,7 @@ static void worker_for(void *_data, long i, int tid) // kt_for() callback
{
step_t *step = (step_t*)_data;
if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
fprintf(stderr, "Processing query %s on thread %d\n", step->seq[i].name, tid);
fprintf(stderr, "QR\t%s\t%d\n", step->seq[i].name, tid);
step->reg[i] = mm_map(step->p->mi, step->seq[i].l_seq, step->seq[i].seq, &step->n_reg[i], step->buf[tid], step->p->opt, step->seq[i].name);
}

1
mmpriv.h
View File

@ -10,6 +10,7 @@
#define MM_DBG_NO_KALLOC 0x1
#define MM_DBG_PRINT_QNAME 0x2
#define MM_DBG_PRINT_SEED 0x4
#ifndef kroundup32
#define kroundup32(x) (--(x), (x)|=(x)>>1, (x)|=(x)>>2, (x)|=(x)>>4, (x)|=(x)>>8, (x)|=(x)>>16, ++(x))