From 6ea66e129040513faa151ffd46e03865ef4490eb Mon Sep 17 00:00:00 2001 From: chhylp123 Date: Tue, 27 Jul 2021 20:11:22 -0400 Subject: [PATCH] resolve conflicts --- CommandLines.h | 2 +- anchor.cpp | 3 ++- htab.cpp | 2 +- sketch.cpp | 19 ------------------- 4 files changed, 4 insertions(+), 22 deletions(-) diff --git a/CommandLines.h b/CommandLines.h index 2fd0fc9..8452f0b 100644 --- a/CommandLines.h +++ b/CommandLines.h @@ -4,7 +4,7 @@ #include #include -#define HA_VERSION "0.15.5-r351" +#define HA_VERSION "0.15.5-r352" #define VERBOSE 0 diff --git a/anchor.cpp b/anchor.cpp index a5f8b26..3cafa97 100644 --- a/anchor.cpp +++ b/anchor.cpp @@ -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; // 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 if (ab->mz.m > ab->old_mz_m) { ab->old_mz_m = ab->mz.m; diff --git a/htab.cpp b/htab.cpp index d56c153..2175ce2 100644 --- a/htab.cpp +++ b/htab.cpp @@ -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); 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); 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); diff --git a/sketch.cpp b/sketch.cpp index 72f9d39..1c5d69b 100644 --- a/sketch.cpp +++ b/sketch.cpp @@ -9,25 +9,6 @@ #define MAX_HIGH_OCC 8 // TODO: don't hard code if we need to tune this parameter #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) {