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Enable building on non-SSE platforms #603

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Enable building on non-SSE platforms #603

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c52752f
Enable building on non-SSE platforms
StuartAbercrombie Jan 22, 2024
085fe23
Update Levenshtein_distance.h
StuartAbercrombie Jan 24, 2024
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27 changes: 21 additions & 6 deletions Correct.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -428,9 +428,15 @@ char* r_string)

if (groupLen == GROUP_SIZE)
{
Reserve_Banded_BPM_4_SSE_only(dumy->overlap_region_group[0], dumy->overlap_region_group[1],
#if defined(__x86_64__) || defined(__x86__)
Reserve_Banded_BPM_4_SSE_only(dumy->overlap_region_group[0], dumy->overlap_region_group[1],
dumy->overlap_region_group[2], dumy->overlap_region_group[3], Window_Len, x_string, WINDOW,
return_sites, return_sites_error, THRESHOLD, dumy->Peq_SSE);
#else
Reserve_Banded_BPM_4(dumy->overlap_region_group[0], dumy->overlap_region_group[1],
dumy->overlap_region_group[2], dumy->overlap_region_group[3], Window_Len, x_string, WINDOW,
return_sites, return_sites_error, THRESHOLD);
#endif
groupLen = 0;


Expand Down Expand Up @@ -485,10 +491,15 @@ char* r_string)
}
else if (groupLen > 1)
{
Reserve_Banded_BPM_4_SSE_only(dumy->overlap_region_group[0], dumy->overlap_region_group[1],
dumy->overlap_region_group[2], dumy->overlap_region_group[3], Window_Len, x_string, WINDOW,
return_sites, return_sites_error, THRESHOLD, dumy->Peq_SSE);

#if defined(__x86_64__) || defined(__x86__)
Reserve_Banded_BPM_4_SSE_only(dumy->overlap_region_group[0], dumy->overlap_region_group[1],
dumy->overlap_region_group[2], dumy->overlap_region_group[3], Window_Len, x_string, WINDOW,
return_sites, return_sites_error, THRESHOLD, dumy->Peq_SSE);
#else
Reserve_Banded_BPM_4(dumy->overlap_region_group[0], dumy->overlap_region_group[1],
dumy->overlap_region_group[2], dumy->overlap_region_group[3], Window_Len, x_string, WINDOW,
return_sites, return_sites_error, THRESHOLD);
#endif
for (i = 0; i < groupLen; i++)
{
if (return_sites_error[i]!=(unsigned int)-1) {
Expand Down Expand Up @@ -9946,10 +9957,12 @@ void clear_Cigar_record(Cigar_record* dummy)
void init_Correct_dumy_buf(Correct_dumy* list, void *km)
{
memset(list, 0, sizeof(Correct_dumy));
#if defined(__x86_64__) || defined(__x86__)
int i;
for (i = 0; i < 256; i++){
list->Peq_SSE[i] = _mm_setzero_si128();
}
#endif
}


Expand All @@ -9960,11 +9973,13 @@ void init_Correct_dumy(Correct_dumy* list)
list->lengthNT = 0;
list->start_i = 0;
list->overlapID = NULL;
#if defined(__x86_64__) || defined(__x86__)
int i;
for (i = 0; i < 256; i++)
{
list->Peq_SSE[i] = _mm_setzero_si128();
}
#endif


list->corrected_read_size = 1000;
Expand Down Expand Up @@ -21441,4 +21456,4 @@ void ug_lalign(overlap_region_alloc* ol, Candidates_list *cl, const ul_idx_t *ur
// fprintf(stderr, "-utg%.6ld%c\tol->length::%lu\n", sid+1, "lc"[uref->ug->u.a[sid].circ], ol->length);
// }
}
}
}
3 changes: 3 additions & 0 deletions Correct.h
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Expand Up @@ -1088,7 +1088,10 @@ typedef struct
/****************************may have bugs********************************/

int path_length;

#if defined(__x86_64__) || defined(__x86__)
__m128i Peq_SSE[256];
#endif
} Correct_dumy;

typedef struct
Expand Down
21 changes: 18 additions & 3 deletions Levenshtein_distance.h
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Original file line number Diff line number Diff line change
Expand Up @@ -3,10 +3,9 @@

#define __STDC_LIMIT_MACROS
#include <stdint.h>
#include "emmintrin.h"
#include "nmmintrin.h"
#include "smmintrin.h"
#if defined(__x86_64__) || defined(__i386__)
#include <immintrin.h>
#endif
#include <string.h>
#include <stdlib.h>
#include <stdio.h>
Expand Down Expand Up @@ -4278,6 +4277,7 @@ inline int Reserve_Banded_BPM_PATH
return return_site;
}

#if defined(__x86_64__) || defined(__i386__)
////four patterns have the same p_length
inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *pattern3, char *pattern4, int p_length, char *text, int t_length,
int* return_sites, unsigned int* return_sites_error, unsigned short errthold, __m128i* Peq_SSE)
Expand Down Expand Up @@ -4585,6 +4585,21 @@ inline int Reserve_Banded_BPM_4_SSE_only(char *pattern1, char *pattern2, char *p

return 1;
}
#else
inline int Reserve_Banded_BPM_4(char *pattern1, char *pattern2, char *pattern3, char *pattern4, int p_length, char *text, int t_length,
int* return_sites, unsigned int* return_sites_error, unsigned short errthold) {
return_sites[0] =
Reserve_Banded_BPM(pattern1, p_length, text, t_length, errthold, &return_sites_error[0]);
return_sites[1] =
Reserve_Banded_BPM(pattern2, p_length, text, t_length, errthold, &return_sites_error[1]);
return_sites[2] =
Reserve_Banded_BPM(pattern3, p_length, text, t_length, errthold, &return_sites_error[2]);
return_sites[3] =
Reserve_Banded_BPM(pattern4, p_length, text, t_length, errthold, &return_sites_error[3]);
return 1;
}
#endif



// void move_trace_gap(uint16_t *trace, int32_t trace_n, int32_t trace_i,
Expand Down
4 changes: 2 additions & 2 deletions Makefile
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@@ -1,6 +1,6 @@
CXX= g++
CC= gcc
CXXFLAGS= -g -O3 -msse4.2 -mpopcnt -fomit-frame-pointer -Wall
CXXFLAGS= -g -march=native -O3 -fomit-frame-pointer -Wall
CFLAGS= $(CXXFLAGS)
CPPFLAGS=
INCLUDES=
Expand Down Expand Up @@ -79,4 +79,4 @@ tovlp.o: tovlp.h
inter.o: inter.h Process_Read.h
kalloc.o: kalloc.h
gfa_ut.o: Overlaps.h
gchain_map.o: gchain_map.h
gchain_map.o: gchain_map.h