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resolve conflicts

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chhylp123
2021-07-27 20:11:22 -04:00
parent 0c81c341d5
commit 6ea66e1290
4 changed files with 4 additions and 22 deletions
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CommandLines.h
+1 -1
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@@ -4,7 +4,7 @@
#include <pthread.h> #include <pthread.h>
#include <stdint.h> #include <stdint.h>
#define HA_VERSION "0.15.5-r351" #define HA_VERSION "0.15.5-r352"
#define VERBOSE 0 #define VERBOSE 0
anchor.cpp
+2 -1
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@@ -255,7 +255,8 @@ kvec_t_u64_warp* chain_idx, void *ha_flt_tab, ha_pt_t *ha_idx, overlap_region* f
ab->mz.n = 0, ab->n_a = 0; ab->mz.n = 0, ab->n_a = 0;
// get the list of anchors // get the list of anchors
ha_sketch_query(u->s, u->len, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, k_flag, dbg_ct); //should use the new version...
///ha_sketch_query(u->s, u->len, asm_opt.mz_win, asm_opt.k_mer_length, 0, !(asm_opt.flag & HA_F_NO_HPC), &ab->mz, ha_flt_tab, k_flag, dbg_ct);
// minimizer of queried read // minimizer of queried read
if (ab->mz.m > ab->old_mz_m) { if (ab->mz.m > ab->old_mz_m) {
ab->old_mz_m = ab->mz.m; ab->old_mz_m = ab->mz.m;
htab.cpp
+1 -1
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@@ -954,7 +954,7 @@ void *ha_ft_ug_gen(const hifiasm_opt_t *asm_opt, ma_utg_v *us, int hap_n)
print_hist_lines(YAK_N_COUNTS, 1, cnt); print_hist_lines(YAK_N_COUNTS, 1, cnt);
ha_ct_shrink(h, cutoff, YAK_MAX_COUNT, asm_opt->thread_num); ha_ct_shrink(h, cutoff, YAK_MAX_COUNT, asm_opt->thread_num);
flt_tab = gen_hh(h); flt_tab = gen_hh(h, asm_opt->max_kmer_cnt);
ha_ct_destroy(h); ha_ct_destroy(h);
fprintf(stderr, "[M::%s::%.3f*%.2f@%.3fGB] ==> filtered out %ld k-mers occurring %d or more times\n", __func__, fprintf(stderr, "[M::%s::%.3f*%.2f@%.3fGB] ==> filtered out %ld k-mers occurring %d or more times\n", __func__,
yak_realtime(), yak_cpu_usage(), yak_peakrss_in_gb(), (long)kh_size(flt_tab), cutoff); yak_realtime(), yak_cpu_usage(), yak_peakrss_in_gb(), (long)kh_size(flt_tab), cutoff);
sketch.cpp
-19
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@@ -9,25 +9,6 @@
#define MAX_HIGH_OCC 8 // TODO: don't hard code if we need to tune this parameter #define MAX_HIGH_OCC 8 // TODO: don't hard code if we need to tune this parameter
#define MAX_MAX_HIGH_OCC 16 #define MAX_MAX_HIGH_OCC 16
typedef struct { // a simplified version of kdq
int front, count;
int a[64];
} tiny_queue_t;
static inline void tq_push(tiny_queue_t *q, int x)
{
q->a[((q->count++) + q->front) & 0x3f] = x;
}
static inline int tq_shift(tiny_queue_t *q)
{
int x;
if (q->count == 0) return -1;
x = q->a[q->front++];
q->front &= 0x3f;
--q->count;
return x;
}
static inline int mzcmp(const ha_mz1_t *a, const ha_mz1_t *b) static inline int mzcmp(const ha_mz1_t *a, const ha_mz1_t *b)
{ {