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make multi

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Saurabh
2021-11-27 10:42:22 -05:00
committed by Heng Li
parent 03540c47b3
commit bedd87f61f
4 changed files with 35 additions and 8 deletions
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Makefile
+16
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@@ -45,6 +45,11 @@ PROG= minimap2
PROG_EXTRA= sdust minimap2-lite PROG_EXTRA= sdust minimap2-lite
LIBS= -lm -lz -lpthread LIBS= -lm -lz -lpthread
CC=$(CXX)
ifeq ($(CC), g++)
CC=g++ -std=c++11
endif
ifeq ($(arm_neon),) # if arm_neon is not defined ifeq ($(arm_neon),) # if arm_neon is not defined
ifeq ($(sse2only),) # if sse2only is not defined ifeq ($(sse2only),) # if sse2only is not defined
OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o ksw2_extd2_avx.o OBJS+=ksw2_extz2_sse41.o ksw2_extd2_sse41.o ksw2_exts2_sse41.o ksw2_extz2_sse2.o ksw2_extd2_sse2.o ksw2_exts2_sse2.o ksw2_dispatch.o ksw2_extd2_avx.o
@@ -93,6 +98,17 @@ libminimap2.a:$(OBJS)
sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h sdust:sdust.c kalloc.o kalloc.h kdq.h kvec.h kseq.h ketopt.h sdust.h
$(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz $(CC) -D_SDUST_MAIN $(CFLAGS) $< kalloc.o -o $@ -lz
multi:
$(MAKE) clean
$(MAKE)
mv minimap2 mm2-fast
$(MAKE) clean
$(MAKE) lhash=1
mv minimap2 mm2-fast-lhash
$(MAKE) clean
$(MAKE) no_opt=1
mv minimap2 mm2-fast-no-opt
# SSE-specific targets on x86/x86_64 # SSE-specific targets on x86/x86_64
ifeq ($(arm_neon),) # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2) ifeq ($(arm_neon),) # if arm_neon is defined, compile this target with the default setting (i.e. no -msse2)
index.c
+2 -1
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@@ -22,7 +22,7 @@
using namespace std; using namespace std;
extern uint64_t minimizer_lookup_time, alignment_time, dp_time, rmq_time, rmq_t1, rmq_t2, rmq_t3, rmq_t4;
#ifdef LISA_HASH #ifdef LISA_HASH
#include "lisa_hash.h" #include "lisa_hash.h"
extern lisa_hash<uint64_t, uint64_t> *lh; extern lisa_hash<uint64_t, uint64_t> *lh;
@@ -479,6 +479,7 @@ void mm_idx_stat(const mm_idx_t *mi)
} }
fprintf(stderr, "[M::%s::%.3f*%.2f] distinct minimizers: %d (%.2f%% are singletons); average occurrences: %.3lf; average spacing: %.3lf; total length: %ld\n", fprintf(stderr, "[M::%s::%.3f*%.2f] distinct minimizers: %d (%.2f%% are singletons); average occurrences: %.3lf; average spacing: %.3lf; total length: %ld\n",
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), n, 100.0*n1/n, (double)sum / n, (double)len / sum, (long)len); __func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), n, 100.0*n1/n, (double)sum / n, (double)len / sum, (long)len);
fprintf(stderr, "minimizer-lookup: %lld dp: %lld rmq: %lld rmq_t1: %lld rmq_t2: %lld rmq_t3: %lld rmq_t4: %lld alignment: %lld \n", minimizer_lookup_time, dp_time, rmq_time, rmq_t1, rmq_t2, rmq_t3, rmq_t4, alignment_time);
} }
int mm_idx_index_name(mm_idx_t *mi) int mm_idx_index_name(mm_idx_t *mi)
map.c
+11 -1
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@@ -9,9 +9,13 @@
#include "mmpriv.h" #include "mmpriv.h"
#include "bseq.h" #include "bseq.h"
#include "khash.h" #include "khash.h"
#include <x86intrin.h>
#ifdef MANUAL_PROFILING
extern uint64_t minimizer_lookup_time;
extern uint64_t rmq_time; extern uint64_t rmq_time;
#endif
struct mm_tbuf_s { struct mm_tbuf_s {
void *km; void *km;
int rep_len, frag_gap; int rep_len, frag_gap;
@@ -175,6 +179,9 @@ static mm128_t *collect_seed_hits_heap(void *km, const mm_mapopt_t *opt, int max
static mm128_t *collect_seed_hits(void *km, const mm_mapopt_t *opt, int max_occ, const mm_idx_t *mi, const char *qname, const mm128_v *mv, int qlen, int64_t *n_a, int *rep_len, static mm128_t *collect_seed_hits(void *km, const mm_mapopt_t *opt, int max_occ, const mm_idx_t *mi, const char *qname, const mm128_v *mv, int qlen, int64_t *n_a, int *rep_len,
int *n_mini_pos, uint64_t **mini_pos) int *n_mini_pos, uint64_t **mini_pos)
{ {
#ifdef MANUAL_PROFILING
uint64_t lookup_start = __rdtsc();
#endif
int i, n_m; int i, n_m;
mm_seed_t *m; mm_seed_t *m;
mm128_t *a; mm128_t *a;
@@ -207,6 +214,9 @@ static mm128_t *collect_seed_hits(void *km, const mm_mapopt_t *opt, int max_occ,
} }
kfree(km, m); kfree(km, m);
radix_sort_128x(a, a + (*n_a)); radix_sort_128x(a, a + (*n_a));
#ifdef MANUAL_PROFILING
minimizer_lookup_time += __rdtsc() - lookup_start;
#endif
return a; return a;
} }
seed.c
+6 -6
View File
@@ -13,9 +13,9 @@ extern uint64_t minimizer_lookup_time;
mm_seed_t *mm_seed_collect_all(void *km, const mm_idx_t *mi, const mm128_v *mv, int32_t *n_m_) mm_seed_t *mm_seed_collect_all(void *km, const mm_idx_t *mi, const mm128_v *mv, int32_t *n_m_)
{ {
#ifdef MANUAL_PROFILING //#ifdef MANUAL_PROFILING
uint64_t lookup_start = __rdtsc(); // uint64_t lookup_start = __rdtsc();
#endif //#endif
#ifdef LISA_HASH #ifdef LISA_HASH
//----------------------------------- //-----------------------------------
@@ -65,9 +65,9 @@ mm_seed_t *mm_seed_collect_all(void *km, const mm_idx_t *mi, const mm128_v *mv,
free(lisa_pos); free(lisa_pos);
#endif #endif
*n_m_ = k; *n_m_ = k;
#ifdef MANUAL_PROFILING //#ifdef MANUAL_PROFILING
minimizer_lookup_time += __rdtsc() - lookup_start; // minimizer_lookup_time += __rdtsc() - lookup_start;
#endif //#endif
return m; return m;
} }