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mm2-fast: Initial commit

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Saurabh
2021-06-14 22:05:08 -07:00
committed by Heng Li
parent b6ff332de1
commit 0369874d4e
13 changed files with 1353 additions and 50 deletions
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3
.gitmodules vendored
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@@ -1,3 +1,6 @@
[submodule "lib/simde"]
path = lib/simde
url = https://github.com/nemequ/simde.git
[submodule "ext/TAL"]
path = ext/TAL
url = https://github.com/IntelLabs/Trans-Omics-Acceleration-Library.git

40
Makefile
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@@ -1,14 +1,44 @@
CFLAGS= -g -Wall -O2 -Wc++-compat #-Wextra
CPPFLAGS= -DHAVE_KALLOC
INCLUDES=
CFLAGS= -Wall -O2 -Wc++-compat #-Wextra
CPPFLAGS= -DHAVE_KALLOC -march=native
OPT_FLAGS= -DVECTORIZED_CHAINING -DALIGN_AVX
ifeq ($(lhash), 1)
OPT_FLAGS+= -DLISA_HASH -DUINT64 -DVECTORIZE
endif
ifeq ($(manual_profile), 1)
CPPFLAGS+= -DMANUAL_PROFILING
endif
ifeq ($(arch), avx512)
CPPFLAGS+= -xCORE-AVX512
endif
ifeq ($(disable_output), 1)
CPPFLAGS+= -DDISABLE_OUTPUT
endif
ifeq ($(no_opt),)
CPPFLAGS+= $(OPT_FLAGS)
endif
INCLUDES= -I./ext/TAL/src/LISA-hash -I./ext/TAL/src/dynamic-programming
OBJS= kthread.o kalloc.o misc.o bseq.o sketch.o sdust.o options.o index.o chain.o align.o hit.o map.o format.o pe.o esterr.o splitidx.o ksw2_ll_sse.o
PROG= minimap2
PROG_EXTRA= sdust minimap2-lite
LIBS= -lm -lz -lpthread
LIBS= -lm -lz -lpthread
CC=$(CXX)
ifeq ($(CC), g++)
CC=g++ -std=c++11
endif
ifeq ($(arm_neon),) # if arm_neon is not defined
ifeq ($(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
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
else # if sse2only is defined
OBJS+=ksw2_extz2_sse.o ksw2_extd2_sse.o ksw2_exts2_sse.o
endif

29
README.md
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@@ -1,3 +1,32 @@
## mm2-fast
### Introduction
mm2-fast is an accelerated implementation of minimap2 on modern CPUs. mm2-fast accelerates all three major modules of minimap2: Seeding, Chaining, and Alignment, achieving upto 3.5x speedup over minimap2.
mm2-fast is a drop-in replacement of minimap2, providing the same functionality with the exact same output.
In the current version, all the modules are optimized using **AVX-512** vectorization. For non-AVX-512 machines, mm2-fast runs as minimap2 code.
### Usage
```sh
git clone --recursive https://github.com/lh3/minimap2.git -b fast-contrib mm2-fast
cd mm2-fast
# Compile and run mm2-fast (without seeding module optimizations).
make clean && make
./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam
# Compile and run mm2-fast (with all three optimized modules)
1. Build learned hash table index for optimized seeding module
Pre-requisite: Install "Rust" and add path to .bashrc file. For Rust installation, visit https://rustup.rs/
./build_rmi.sh ref.fa map-ont ##takes two arguments: 1. path-to-reference-seq-file 2. preset
2. Compile and run
make clean && make lhash=1
./minimap2 -ax map-ont ref.fa ont.fq.gz > aln.sam
# Compile with all optimizations disabled (runs as minimap2)
make clean && make no_opt=1
```
The original README content of minimap2 follows.
[![GitHub Downloads](https://img.shields.io/github/downloads/lh3/minimap2/total.svg?style=social&logo=github&label=Download)](https://github.com/lh3/minimap2/releases)
[![BioConda Install](https://img.shields.io/conda/dn/bioconda/minimap2.svg?style=flag&label=BioConda%20install)](https://anaconda.org/bioconda/minimap2)
[![PyPI](https://img.shields.io/pypi/v/mappy.svg?style=flat)](https://pypi.python.org/pypi/mappy)

52
align.c
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@@ -1,3 +1,33 @@
/* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2017-2018 Broad Institute, Inc.
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Modified Copyright (C) 2021 Intel Corporation
Contacts: Saurabh Kalikar <saurabh.kalikar@intel.com>;
Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
Chirag Jain <chirag@iisc.ac.in>; Heng Li <hli@jimmy.harvard.edu>
*/
#include <assert.h>
#include <string.h>
#include <stdlib.h>
@@ -5,7 +35,9 @@
#include "minimap.h"
#include "mmpriv.h"
#include "ksw2.h"
#include "ksw2_extd2_avx.h"
#include <x86intrin.h>
extern uint64_t alignment_time;
static void ksw_gen_simple_mat(int m, int8_t *mat, int8_t a, int8_t b, int8_t sc_ambi)
{
int i, j;
@@ -312,6 +344,10 @@ static void mm_append_cigar(mm_reg1_t *r, uint32_t n_cigar, uint32_t *cigar) //
static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint8_t *qseq, int tlen, const uint8_t *tseq, const uint8_t *junc, const int8_t *mat, int w, int end_bonus, int zdrop, int flag, ksw_extz_t *ez)
{
#ifdef MANUAL_PROFILING
uint64_t align_start = __rdtsc();
#endif
if (mm_dbg_flag & MM_DBG_PRINT_ALN_SEQ) {
int i;
fprintf(stderr, "===> q=(%d,%d), e=(%d,%d), bw=%d, flag=%d, zdrop=%d <===\n", opt->q, opt->q2, opt->e, opt->e2, w, flag, opt->zdrop);
@@ -327,8 +363,17 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
ksw_exts2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->noncan, zdrop, opt->junc_bonus, flag, junc, ez);
else if (opt->q == opt->q2 && opt->e == opt->e2)
ksw_extz2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, w, zdrop, end_bonus, flag, ez);
else
else{
#ifdef ALIGN_AVX
#ifdef __AVX512BW__
ksw_extd2_avx512(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->e2, w, zdrop, end_bonus, flag, ez);
#else
ksw_extd2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->e2, w, zdrop, end_bonus, flag, ez);
#endif
#else
ksw_extd2_sse(km, qlen, qseq, tlen, tseq, 5, mat, opt->q, opt->e, opt->q2, opt->e2, w, zdrop, end_bonus, flag, ez);
#endif
}
if (mm_dbg_flag & MM_DBG_PRINT_ALN_SEQ) {
int i;
fprintf(stderr, "score=%d, cigar=", ez->score);
@@ -336,6 +381,9 @@ static void mm_align_pair(void *km, const mm_mapopt_t *opt, int qlen, const uint
fprintf(stderr, "%d%c", ez->cigar[i]>>4, "MIDN"[ez->cigar[i]&0xf]);
fprintf(stderr, "\n");
}
#ifdef MANUAL_PROFILING
alignment_time += (__rdtsc() - align_start);
#endif
}
static inline int mm_get_hplen_back(const mm_idx_t *mi, uint32_t rid, uint32_t x)

17
build_rmi.sh Executable file
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@@ -0,0 +1,17 @@
ref_data=$1
preset=$2
make clean && make no_opt=1
touch temp_read.fastq
./minimap2 -ax $2 $1 temp_read.fastq -Z 1 >/dev/null
kv_file=$1"_"$2"_minimizers_key_value_sorted"
full_path=`readlink -f $kv_file`
cd ./ext/TAL
make lisa_hash
./build-lisa-hash-index $kv_file
rm ../../temp_read.fastq

61
chain.c
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@@ -1,10 +1,39 @@
/* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2017-2018 Broad Institute, Inc.
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Modified Copyright (C) 2021 Intel Corporation
Contacts: Saurabh Kalikar <saurabh.kalikar@intel.com>;
Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
Chirag Jain <chirag@iisc.ac.in>; Heng Li <hli@jimmy.harvard.edu>
*/
#include <stdint.h>
#include <string.h>
#include <stdio.h>
#include "minimap.h"
#include "mmpriv.h"
#include "kalloc.h"
#include "parallel_chaining_32_bit.h"
static const char LogTable256[256] = {
#define LT(n) n, n, n, n, n, n, n, n, n, n, n, n, n, n, n, n
-1, 0, 1, 1, 2, 2, 2, 2, 3, 3, 3, 3, 3, 3, 3, 3,
@@ -19,9 +48,11 @@ static inline int ilog2_32(uint32_t v)
return (t = v>>8) ? 8 + LogTable256[t] : LogTable256[v];
}
mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int max_iter, int min_cnt, int min_sc, float gap_scale, int is_cdna, int n_segs, int64_t n, mm128_t *a, int *n_u_, uint64_t **_u, void *km)
{ // TODO: make sure this works when n has more than 32 bits
int32_t k, *f, *p, *t, *v, n_u, n_v;
int32_t k, *p, *t, *v, n_u, n_v;
uint32_t *f;
int64_t i, j, st = 0;
uint64_t *u, *u2, sum_qspan = 0;
float avg_qspan;
@@ -32,11 +63,33 @@ mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int m
kfree(km, a);
return 0;
}
f = (int32_t*)kmalloc(km, n * 4);
f = (uint32_t*)kmalloc(km, n * 4);
p = (int32_t*)kmalloc(km, n * 4);
t = (int32_t*)kmalloc(km, n * 4);
v = (int32_t*)kmalloc(km, n * 4);
memset(t, 0, n * 4);
#if VECTORIZED_CHAINING
anchor_t* anchors = (anchor_t*)malloc(n* sizeof(anchor_t));
for (i = 0; i < n; ++i) {
uint64_t ri = a[i].x;
int32_t qi = (int32_t)a[i].y, q_span = a[i].y>>32&0xff; // NB: only 8 bits of span is used!!!
anchors[i].r = ri;
anchors[i].q = qi;
anchors[i].l = q_span;
}
num_bits_t *anchor_r, *anchor_q, *anchor_l;
create_SoA_Anchors_32_bit(anchors, n, anchor_r, anchor_q, anchor_l);
dp_chain obj(max_dist_x, max_dist_y, bw, max_skip, max_iter, gap_scale, is_cdna, n_segs);
obj.mm_dp_vectorized(n, &anchors[0], anchor_r, anchor_q, anchor_l, f, p, v, max_dist_x, max_dist_y, NULL, NULL);
// -16 is due to extra padding at the start of arrays
anchor_r -= 16; anchor_q -= 16; anchor_l -= 16;
free(anchor_r);
free(anchor_q);
free(anchor_l);
free(anchors);
#else
for (i = 0; i < n; ++i) sum_qspan += a[i].y>>32&0xff;
avg_qspan = (float)sum_qspan / n;
@@ -85,7 +138,7 @@ mm128_t *mm_chain_dp(int max_dist_x, int max_dist_y, int bw, int max_skip, int m
f[i] = max_f, p[i] = max_j;
v[i] = max_j >= 0 && v[max_j] > max_f? v[max_j] : max_f; // v[] keeps the peak score up to i; f[] is the score ending at i, not always the peak
}
#endif
// find the ending positions of chains
memset(t, 0, n * 4);
for (i = 0; i < n; ++i)

1
ext/TAL Submodule

Submodule ext/TAL added at 75ce461846

139
index.c
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@@ -1,4 +1,37 @@
/* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2017-2018 Broad Institute, Inc.
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Modified Copyright (C) 2021 Intel Corporation
Contacts: Saurabh Kalikar <saurabh.kalikar@intel.com>;
Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
Chirag Jain <chirag@iisc.ac.in>; Heng Li <hli@jimmy.harvard.edu>
*/
#include <stdlib.h>
#include<map>
#include <vector>
#include <fstream>
using namespace std;
#include <assert.h>
#if defined(WIN32) || defined(_WIN32)
#include <io.h> // for open(2)
@@ -53,6 +86,37 @@ mm_idx_t *mm_idx_init(int w, int k, int b, int flag)
return mi;
}
void mm_idx_destroy_mm_hash(mm_idx_t *mi)
{
uint32_t i;
if (mi == 0) return;
if (mi->h) kh_destroy(str, (khash_t(str)*)mi->h);
if (mi->B) {
for (i = 0; i < 1U<<mi->b; ++i) {
free(mi->B[i].p);
free(mi->B[i].a.a);
kh_destroy(idx, (idxhash_t*)mi->B[i].h);
}
}
}
void mm_idx_destroy_seq(mm_idx_t *mi)
{
uint32_t i;
if (mi->I) {
for (i = 0; i < mi->n_seq; ++i)
free(mi->I[i].a);
free(mi->I);
}
if (!mi->km) {
for (i = 0; i < mi->n_seq; ++i)
free(mi->seq[i].name);
free(mi->seq);
} else km_destroy(mi->km);
free(mi->B); free(mi->S); free(mi);
}
void mm_idx_destroy(mm_idx_t *mi)
{
uint32_t i;
@@ -97,6 +161,81 @@ const uint64_t *mm_idx_get(const mm_idx_t *mi, uint64_t minier, int *n)
}
}
//Output minimap2's hash table entries
void mm_idx_dump_hash(const char* f_name, const mm_idx_t *mi)
{
std::map<uint64_t, vector<uint64_t>> m;
ofstream f(f_name);
fprintf(stderr, "Building sorted key-val map");
uint32_t i,j;
uint64_t num_values = 0;
for (i = 0; i < 1U<<mi->b; ++i) {
//fprintf(stderr, "BucketID %lu \n", i);
idxhash_t *h = (idxhash_t*)mi->B[i].h;
khint_t k;
if (h == 0) continue;
for (k = 0; k < kh_end(h); ++k){
if (kh_exist(h, k)) {
uint64_t key = kh_key(h, k), bucket_id = i;
key = key>>1;
key = key<<mi->b | bucket_id;
if(kh_key(h, k)&1)
{
//print key value
//fprintf(stderr, "%llu %llu %llu\n", key, kh_val(h, k), 0);
m[key].push_back(kh_val(h, k));
}
else
{ // print key
uint32_t n = (uint32_t)kh_val(h, k);
//fprintf(stderr, "%llu %llu %llu ", key, kh_val(h, k), n);
// for 0 to lsb 32 val
// print b->p[msb 32 of val]
for(j = 0; j < n; j++)
{
//fprintf(stderr, "%llu ", mi->B[i].p[(kh_val(h, k)>>32) + j]);
m[key].push_back(mi->B[i].p[(kh_val(h, k)>>32) + j]);
}
}
}
}
}
fprintf(stderr, "Storing hash to %s \n", f_name);
vector<uint64_t> key_list;
key_list.push_back(m.size());
for(auto k : m){
key_list.push_back(k.first);
f<<k.first << " "<<k.second.size()<<endl;
for(int j = 0; j < k.second.size(); j++){
f<<k.second[j]<<" ";
num_values++;
}
f<<endl;
}
f.close();
string size_file_name = (string) f_name + "_size";
ofstream size_f(size_file_name);
size_f<<m.size()<<" "<<num_values;
size_f.close();
string prefix = (string)f_name + "_keys";
string keys_bin_file_name = prefix + ".uint64";
ofstream wf(keys_bin_file_name, ios::out | ios::binary);
wf.write((char*)&key_list[0], (key_list.size())*sizeof(uint64_t));
wf.close();
key_list.clear();
m.clear();
}
void mm_idx_stat(const mm_idx_t *mi)
{
int n = 0, n1 = 0;

664
ksw2_extd2_avx.c Normal file
View File

@@ -0,0 +1,664 @@
/* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2017-2018 Broad Institute, Inc.
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Modified Copyright (C) 2021 Intel Corporation
Contacts: Saurabh Kalikar <saurabh.kalikar@intel.com>;
Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
Chirag Jain <chirag@iisc.ac.in>; Heng Li <hli@jimmy.harvard.edu>
*/
#include "ksw2_extd2_avx.h"
#ifdef __AVX512BW__
void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez)
{
__m512i ind512_srli = _mm512_set1_epi8(15);
__mmask8 msk_srli = 0x0003;
__m512i bt32_ = _mm512_setr_epi32(0,0,0,0,4,4,4,4,8,8,8,8,12,12,12,12);
int8_t index[64] __attribute((aligned(64)));
for (int i=0; i<64; i++)
index[i] = i%16 - 1;
index[0] = 15;
index[16] = 31;
index[32] = 47;
index[48] = 63;
__m512i shf512a, shf512b, slli512;
__m512i ind512_slli = _mm512_load_si512((__m512i*) index);
__mmask8 mska = 0x90;
__mmask64 mskb = 0x0001000100010000;
__mmask64 mskc = 0x1;
__mmask64 mskc_ar[4] = {0x1, 0x10000, 0x100000000, 0x1000000000000};
#define __dp_code_block1_pcl \
/*__mmask64 mskc_ = mskc; */ \
/*if (t == st_) */ \
__mmask64 mskc_ = (t == st_) ? mskc_ar[(st0 - t*64)/16]:mskc; \
z = _mm512_load_si512(&s[t]); \
xt1 = _mm512_load_si512(&x[t]); /* xt1 <- x[r-1][t..t+15] */ \
/* tmp = _mm_srli_si128(xt1, 15); */ /* tmp <- x[r-1][t+15] */ \
tmp = _mm512_set1_epi8(((int8_t*)x)[t*64 + 63]); \
/* xt1 = _mm_or_si128(_mm_slli_si128(xt1, 1), x1_);*/ /* xt1 <- x[r-1][t-1..t+14] */ \
shf512a = _mm512_shuffle_epi8(xt1, ind512_slli); \
shf512b = _mm512_shuffle_i32x4(shf512a, shf512a, mska); \
slli512 = _mm512_mask_blend_epi8(mskb, shf512a, shf512b); \
xt1 = _mm512_mask_blend_epi8(mskc_, slli512, x1_); \
x1_ = tmp; \
vt1 = _mm512_load_si512(&v[t]); /* vt1 <- v[r-1][t..t+15] */ \
/* tmp = _mm_srli_si128(vt1, 15); */ /* tmp <- v[r-1][t+15] */ \
tmp = _mm512_set1_epi8(((int8_t*)v)[t*64 + 63]); \
/* vt1 = _mm_or_si128(_mm_slli_si128(vt1, 1), v1_); *//* vt1 <- v[r-1][t-1..t+14] */ \
shf512a = _mm512_shuffle_epi8(vt1, ind512_slli); \
shf512b = _mm512_shuffle_i32x4(shf512a, shf512a, mska); \
slli512 = _mm512_mask_blend_epi8(mskb, shf512a, shf512b); \
vt1 = _mm512_mask_blend_epi8(mskc_, slli512, v1_); \
v1_ = tmp; \
a = _mm512_add_epi8(xt1, vt1); /* a <- x[r-1][t-1..t+14] + v[r-1][t-1..t+14] */ \
ut = _mm512_load_si512(&u[t]); /* ut <- u[t..t+15] */ \
b = _mm512_add_epi8(_mm512_load_si512(&y[t]), ut); /* b <- y[r-1][t..t+15] + u[r-1][t..t+15] */ \
x2t1= _mm512_load_si512(&x2[t]); \
/* tmp = _mm_srli_si128(x2t1, 15);*/ \
tmp = _mm512_set1_epi8(((int8_t*)x2)[t*64 + 63]); \
/* x2t1= _mm_or_si128(_mm_slli_si128(x2t1, 1), x21_); */ \
shf512a = _mm512_shuffle_epi8(x2t1, ind512_slli); \
shf512b = _mm512_shuffle_i32x4(shf512a, shf512a, mska); \
slli512 = _mm512_mask_blend_epi8(mskb, shf512a, shf512b); \
x2t1 = _mm512_mask_blend_epi8(mskc_, slli512, x21_); \
x21_= tmp; \
a2= _mm512_add_epi8(x2t1, vt1); \
b2= _mm512_add_epi8(_mm512_load_si512(&y2[t]), ut);
#define __dp_code_block2_pcl \
_mm512_store_si512(&u[t], _mm512_sub_epi8(z, vt1)); /* u[r][t..t+15] <- z - v[r-1][t-1..t+14] */ \
_mm512_store_si512(&v[t], _mm512_sub_epi8(z, ut)); /* v[r][t..t+15] <- z - u[r-1][t..t+15] */ \
tmp = _mm512_sub_epi8(z, q_); \
a = _mm512_sub_epi8(a, tmp); \
b = _mm512_sub_epi8(b, tmp); \
tmp = _mm512_sub_epi8(z, q2_); \
a2= _mm512_sub_epi8(a2, tmp); \
b2= _mm512_sub_epi8(b2, tmp);
__mmask64 msk_ar[5] = {0xFFFF, 0xFFFFFFFF, 0xFFFFFFFFFFFF, 0xFFFFFFFFFFFFFFFF, 0xFFFFFFFFFFFFFFFF};
__mmask64 msk_ar2[5] = {0xFFFF, 0xFFFF, 0xFFFFFFFF, 0xFFFFFFFFFFFF, 0xFFFFFFFFFFFFFFFF};
int r, t, qe = q + e, n_col_, *off = 0, *off_end = 0, tlen_, qlen_, last_st, last_en, wl, wr, max_sc, min_sc, long_thres, long_diff;
int with_cigar = !(flag&KSW_EZ_SCORE_ONLY), approx_max = !!(flag&KSW_EZ_APPROX_MAX);
int32_t *H = 0, H0 = 0, last_H0_t = 0;
uint8_t *qr, *sf, *mem, *mem2 = 0;
__m512i q_, q2_, qe_, qe2_, zero_, sc_mch_, sc_mis_, m1_, sc_N_;
__m512i *u, *v, *x, *y, *x2, *y2, *s, *p = 0;
__m512i one_, two_, three_, four_, s1_, s2_, s3_, s4_;
ksw_reset_extz(ez);
if (m <= 1 || qlen <= 0 || tlen <= 0) return;
if (q2 + e2 < q + e) t = q, q = q2, q2 = t, t = e, e = e2, e2 = t; // make sure q+e no larger than q2+e2
s1_ = _mm512_set1_epi8(0x08);
s2_ = _mm512_set1_epi8(0x10);
s3_ = _mm512_set1_epi8(0x20);
s4_ = _mm512_set1_epi8(0x40);
one_ = _mm512_set1_epi8(1);
two_ = _mm512_set1_epi8(2);
three_ = _mm512_set1_epi8(3);
four_ = _mm512_set1_epi8(4);
zero_ = _mm512_set1_epi8(0);
q_ = _mm512_set1_epi8(q);
q2_ = _mm512_set1_epi8(q2);
qe_ = _mm512_set1_epi8(q + e);
qe2_ = _mm512_set1_epi8(q2 + e2);
sc_mch_ = _mm512_set1_epi8(mat[0]);
sc_mis_ = _mm512_set1_epi8(mat[1]);
sc_N_ = mat[m*m-1] == 0? _mm512_set1_epi8(-e2) : _mm512_set1_epi8(mat[m*m-1]);
m1_ = _mm512_set1_epi8(m - 1); // wildcard
if (w < 0) w = tlen > qlen? tlen : qlen;
wl = wr = w;
tlen_ = (tlen + 63) / 64;
n_col_ = qlen < tlen? qlen : tlen;
n_col_ = ((n_col_ < w + 1? n_col_ : w + 1) + 63) / 64 + 1;
qlen_ = (qlen + 63) / 64;
for (t = 1, max_sc = mat[0], min_sc = mat[1]; t < m * m; ++t) {
max_sc = max_sc > mat[t]? max_sc : mat[t];
min_sc = min_sc < mat[t]? min_sc : mat[t];
}
if (-min_sc > 2 * (q + e)) return; // otherwise, we won't see any mismatches
long_thres = e != e2? (q2 - q) / (e - e2) - 1 : 0;
if (q2 + e2 + long_thres * e2 > q + e + long_thres * e)
++long_thres;
long_diff = long_thres * (e - e2) - (q2 - q) - e2;
mem = (uint8_t*)kcalloc(km, tlen_ * 8 + qlen_ + 1 + 63, 64);
u = (__m512i*)(((size_t)mem + 63) >> 6 << 6); // 16-byte aligned
v = u + tlen_, x = v + tlen_, y = x + tlen_, x2 = y + tlen_, y2 = x2 + tlen_;
s = y2 + tlen_, sf = (uint8_t*)(s + tlen_), qr = sf + tlen_ * 64;
memset(u, -q - e, tlen_ * 64);
memset(v, -q - e, tlen_ * 64);
memset(x, -q - e, tlen_ * 64);
memset(y, -q - e, tlen_ * 64);
memset(x2, -q2 - e2, tlen_ * 64);
memset(y2, -q2 - e2, tlen_ * 64);
if (!approx_max) {
H = (int32_t*)kmalloc(km, tlen_ * 64 * 4);
for (t = 0; t < tlen_ * 64; ++t) H[t] = KSW_NEG_INF;
}
if (with_cigar) {
mem2 = (uint8_t*)kmalloc(km, ((size_t)(qlen + tlen - 1) * n_col_ + 1) * 64);
p = (__m512i*)(((size_t)mem2 + 63) >> 6 << 6);
off = (int*)kmalloc(km, (qlen + tlen - 1) * sizeof(int) * 2);
off_end = off + qlen + tlen - 1;
}
for (t = 0; t < qlen; ++t) qr[t] = query[qlen - 1 - t];
memcpy(sf, target, tlen);
for (r = 0, last_st = last_en = -1; r < qlen + tlen - 1; ++r) {
int st = 0, en = tlen - 1, st0, en0, st_, en_;
int8_t x1, x21, v1;
uint8_t *qrr = qr + (qlen - 1 - r);
int8_t *u8 = (int8_t*)u, *v8 = (int8_t*)v, *x8 = (int8_t*)x, *x28 = (int8_t*)x2;
__m512i x1_, x21_, v1_;
// find the boundaries
if (st < r - qlen + 1) st = r - qlen + 1;
if (en > r) en = r;
if (st < (r-wr+1)>>1) st = (r-wr+1)>>1; // take the ceil
if (en > (r+wl)>>1) en = (r+wl)>>1; // take the floor
if (st > en) {
ez->zdropped = 1;
break;
}
st0 = st, en0 = en;
int st_new = st / 16 * 16, en_new = (en + 16) / 16 * 16 - 1;
// int st_new = st / 64 * 64, en_new = (en + 64) / 64 * 64 - 1;
int stb = st, enb = en;
st = st / 64 * 64, en = (en + 64) / 64 * 64 - 1;
int stn = stb / 16 * 16, enn = (enb + 16) / 16 * 16 - 1;
// set boundary conditions
if (st_new > 0) {
if (st_new - 1 >= last_st && st_new - 1 <= last_en) {
x1 = x8[st_new - 1], x21 = x28[st_new - 1], v1 = v8[st_new - 1]; // (r-1,s-1) calculated in the last round
} else {
x1 = -q - e, x21 = -q2 - e2;
v1 = -q - e;
}
} else {
x1 = -q - e, x21 = -q2 - e2;
v1 = r == 0? -q - e : r < long_thres? -e : r == long_thres? long_diff : -e2;
}
if (en_new >= r) {
((int8_t*)y)[r] = -q - e, ((int8_t*)y2)[r] = -q2 - e2;
u8[r] = r == 0? -q - e : r < long_thres? -e : r == long_thres? long_diff : -e2;
}
// loop fission: set scores first
if (!(flag & KSW_EZ_GENERIC_SC)) {
for (t = st0; t <= en0; t += 64) {
__m512i sq, st, tmp_512, mask_512;
__mmask64 tmp, mask;
sq = _mm512_loadu_si512((__m512i*)&sf[t]);
st = _mm512_loadu_si512((__m512i*)&qrr[t]);
// mask = _mm512_or_si512(_mm_cmpeq_epi8(sq, m1_), _mm_cmpeq_epi8(st, m1_));
mask = (_mm512_cmpeq_epi8_mask(sq, m1_) | _mm512_cmpeq_epi8_mask(st, m1_));
tmp = _mm512_cmpeq_epi8_mask(sq, st);
tmp_512 = _mm512_mask_blend_epi8(tmp, sc_mis_, sc_mch_);
tmp_512 = _mm512_mask_blend_epi8(mask, tmp_512, sc_N_);
if (t + 64 > en0)
{
__mmask64 msk;
int ind = (en0 - t + 16)/16;
//assert(ind >= 0 && ind < 5);
msk = msk_ar2[ind];
_mm512_mask_storeu_epi8((__m512i*)((int8_t*)s + t), msk, tmp_512);
}
else
_mm512_storeu_si512((__m512i*)((int8_t*)s + t), tmp_512);
}
} else {
for (t = st0; t <= en0; ++t)
((uint8_t*)s)[t] = mat[sf[t] * m + qrr[t]];
}
// core loop
// fprintf(stderr, "- r: %d, x1: %d, x21: %d, v1: %d, en_new: %d, e: %d, q: %d\n",
//r, x1, x21, v1, en_new, e, q);
x1_ = _mm512_set1_epi8((uint8_t)x1);
x21_ = _mm512_set1_epi8((uint8_t)x21);
v1_ = _mm512_set1_epi8((uint8_t)v1);
//st_ = st / 16, en_ = en / 16;
st_ = st / 64, en_ = en / 64;
//assert(en_ - st_ + 1 <= n_col_);
if (!with_cigar) { // score only
for (t = st_; t <= en_; ++t) {
__m512i z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
__dp_code_block1_pcl;
z = _mm512_max_epi8(z, a);
z = _mm512_max_epi8(z, b);
z = _mm512_max_epi8(z, a2);
z = _mm512_max_epi8(z, b2);
z = _mm512_min_epi8(z, sc_mch_);
// __dp_code_block2_pcl; // save u[] and v[]; update a, b, a2 and b2
if (t == en_) {
__mmask64 msk;
int ind = (en0 - t*64 + 16)/16;
msk = msk_ar2[ind];
// fprintf(stderr, "en0: %d, t: %d, ind: %d, msk: %d\n", en0, t, ind, msk);
_mm512_mask_storeu_epi8(&u[t], msk, _mm512_sub_epi8(z, vt1));
_mm512_mask_storeu_epi8(&v[t], msk, _mm512_sub_epi8(z, ut));
tmp = _mm512_sub_epi8(z, q_);
a = _mm512_sub_epi8(a, tmp);
b = _mm512_sub_epi8(b, tmp);
tmp = _mm512_sub_epi8(z, q2_);
a2= _mm512_sub_epi8(a2, tmp);
b2= _mm512_sub_epi8(b2, tmp);
}
else {
_mm512_store_si512(&u[t], _mm512_sub_epi8(z, vt1));
_mm512_store_si512(&v[t], _mm512_sub_epi8(z, ut));
tmp = _mm512_sub_epi8(z, q_);
a = _mm512_sub_epi8(a, tmp);
b = _mm512_sub_epi8(b, tmp);
tmp = _mm512_sub_epi8(z, q2_);
a2= _mm512_sub_epi8(a2, tmp);
b2= _mm512_sub_epi8(b2, tmp);
}
if (t == en_) {
__mmask64 msk;
int ind = (en0 - t*64 + 16)/16;
//assert(ind >= 0);
msk = msk_ar2[ind];
// fprintf(stderr, "en0: %d, t: %d, ind: %d, msk: %d\n", en0, t, ind, msk);
_mm512_mask_storeu_epi8(&x[t], msk, _mm512_sub_epi8(_mm512_max_epi8(a, zero_), qe_));
_mm512_mask_storeu_epi8(&y[t], msk, _mm512_sub_epi8(_mm512_max_epi8(b, zero_), qe_));
_mm512_mask_storeu_epi8(&x2[t], msk, _mm512_sub_epi8(_mm512_max_epi8(a2, zero_), qe2_));
_mm512_mask_storeu_epi8(&y2[t], msk, _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe2_));
}
else
{
_mm512_store_si512(&x[t], _mm512_sub_epi8(_mm512_max_epi8(a, zero_), qe_));
_mm512_store_si512(&y[t], _mm512_sub_epi8(_mm512_max_epi8(b, zero_), qe_));
_mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_max_epi8(a2, zero_), qe2_));
_mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_max_epi8(b2, zero_), qe2_));
}
// for (int l=0; l<64; l++)
// fprintf(stderr, "%d ", ((int8_t*)x)[l]);
}
} else if (!(flag&KSW_EZ_RIGHT)) { // gap left-alignment
__m512i *pr = p + (size_t)r * n_col_ - st_;
off[r] = st, off_end[r] = en;
for (t = st_; t < en_; ++t) {
__m512i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
__mmask64 tmp_mask;
__dp_code_block1_pcl;
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(a, z),zero_, one_); // d = a > z? 1 : 0
z = _mm512_max_epi8(z, a);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(b, z), d, two_); // d = b > z? 2 : d
z = _mm512_max_epi8(z, b);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(a2, z), d, three_); // d = a2 > z? 3 : d
z = _mm512_max_epi8(z, a2);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(b2, z), d, four_); // d = b2 > z? 4 : d
z = _mm512_max_epi8(z, b2);
z = _mm512_min_epi8(z, sc_mch_);
// __dp_code_block2_pcl;
_mm512_store_si512(&u[t], _mm512_sub_epi8(z, vt1));
_mm512_store_si512(&v[t], _mm512_sub_epi8(z, ut));
tmp = _mm512_sub_epi8(z, q_);
a = _mm512_sub_epi8(a, tmp);
b = _mm512_sub_epi8(b, tmp);
tmp = _mm512_sub_epi8(z, q2_);
a2= _mm512_sub_epi8(a2, tmp);
b2= _mm512_sub_epi8(b2, tmp);
tmp_mask = _mm512_cmpgt_epi8_mask(a, zero_);
_mm512_store_si512(&x[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, a), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s1_)); // d = a > 0? 1<<3 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(b, zero_);
_mm512_store_si512(&y[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, b), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s2_)); // d = b > 0? 1<<4 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(a2, zero_);
_mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, a2), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s3_)); // d = a > 0? 1<<5 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(b2, zero_);
_mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, b2), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s4_)); // d = b > 0? 1<<6 : 0
_mm512_store_si512(&pr[t], d);
}
{
__m512i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
__mmask64 tmp_mask;
__dp_code_block1_pcl;
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(a, z),zero_, one_); // d = a > z? 1 : 0
z = _mm512_max_epi8(z, a);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(b, z), d, two_); // d = b > z? 2 : d
z = _mm512_max_epi8(z, b);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(a2, z), d, three_); // d = a2 > z? 3 : d
z = _mm512_max_epi8(z, a2);
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(b2, z), d, four_); // d = b2 > z? 3 : d
z = _mm512_max_epi8(z, b2);
z = _mm512_min_epi8(z, sc_mch_);
// __dp_code_block2_pcl;
{
__mmask64 msk;
int ind = (en0 - t*64 + 16)/16;
// //assert(ind >= 0 && ind < 5);
msk = msk_ar2[ind];
_mm512_mask_storeu_epi8(&u[t], msk, _mm512_sub_epi8(z, vt1));
_mm512_mask_storeu_epi8(&v[t], msk, _mm512_sub_epi8(z, ut));
tmp = _mm512_sub_epi8(z, q_);
a = _mm512_sub_epi8(a, tmp);
b = _mm512_sub_epi8(b, tmp);
tmp = _mm512_sub_epi8(z, q2_);
a2= _mm512_sub_epi8(a2, tmp);
b2= _mm512_sub_epi8(b2, tmp);
}
{
__mmask64 msk;
int ind = (en0 - t*64 + 16)/16;
msk = msk_ar2[ind];
off_end[r] -= (4-ind)*16;
tmp_mask = _mm512_cmpgt_epi8_mask(a, zero_);
_mm512_mask_storeu_epi8(&x[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, a), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s1_)); // d = a > 0? 1<<3 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(b, zero_);
_mm512_mask_storeu_epi8(&y[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, b), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s2_)); // d = b > 0? 1<<4 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(a2, zero_);
_mm512_mask_storeu_epi8(&x2[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, a2), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s3_)); // d = a > 0? 1<<5 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(b2, zero_);
_mm512_mask_storeu_epi8(&y2[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, zero_, b2), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, zero_, s4_)); // d = b > 0? 1<<6 : 0
//_mm512_store_si512(&pr[t], d);
_mm512_mask_storeu_epi8(&pr[t], msk, d);
}
}
} else { // gap right-alignment
__m512i *pr = p + (size_t)r * n_col_ - st_;
off[r] = st, off_end[r] = en;
// off[r] = stn, off_end[r] = enn;
// fprintf(stderr, "t: %d, st0: %d\n", st_, st0);
for (t = st_; t < en_; ++t) {
__m512i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
__mmask64 tmp_mask;
__dp_code_block1_pcl;
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, a), one_, zero_);
z = _mm512_max_epi8(z, a);
// d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, b), _mm512_set1_epi8(2), d);
// d = z > b? d : 2
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, b), two_, d); // d = z > b? d : 2
z = _mm512_max_epi8(z, b);
// d = z > a2? d : 3
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, a2), three_, d); // d = z > a2? d : 3
z = _mm512_max_epi8(z, a2);
// d = z > b2? d : 4
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, b2), four_, d); // d = z > b2? d : 4
z = _mm512_max_epi8(z, b2);
z = _mm512_min_epi8(z, sc_mch_);
// __dp_code_block2_pcl;
__mmask64 msk;
{
_mm512_store_si512(&u[t], _mm512_sub_epi8(z, vt1));
_mm512_store_si512(&v[t], _mm512_sub_epi8(z, ut));
tmp = _mm512_sub_epi8(z, q_);
a = _mm512_sub_epi8(a, tmp);
b = _mm512_sub_epi8(b, tmp);
tmp = _mm512_sub_epi8(z, q2_);
a2= _mm512_sub_epi8(a2, tmp);
b2= _mm512_sub_epi8(b2, tmp);
}
{
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, a);
_mm512_store_si512(&x[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, a, zero_), qe_));
// d = a > 0? 1<<3 : 0
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, s1_, zero_)); // d = a > 0? 1<<3 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, b);
_mm512_store_si512(&y[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, b, zero_), qe_));
// d = b > 0? 1<<4 : 0
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, s2_, zero_)); // d = b > 0? 1<<4 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, a2);
_mm512_store_si512(&x2[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, a2, zero_), qe2_));
// d = a > 0? 1<<5 : 0
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, s3_, zero_)); // d = a > 0? 1<<5 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, b2);
_mm512_store_si512(&y2[t], _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, b2, zero_), qe2_));
// d = b > 0? 1<<6 : 0
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, s4_, zero_)); // d = b > 0? 1<<6 : 0
_mm512_store_si512(&pr[t], d);
}
}
//for (t = st_; t <= en_; ++t)// Last iteration unrolled
{
__m512i d, z, a, b, a2, b2, xt1, x2t1, vt1, ut, tmp;
__mmask64 tmp_mask;
__dp_code_block1_pcl;
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, a), one_, zero_);
z = _mm512_max_epi8(z, a);
// d = z > b? d : 2
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, b), two_, d); // d = z > b? d : 2
z = _mm512_max_epi8(z, b);
// d = z > a2? d : 3
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, a2), three_, d); // d = z > a2? d : 3
z = _mm512_max_epi8(z, a2);
// d = z > b2? d : 4
d = _mm512_mask_blend_epi8(_mm512_cmpgt_epi8_mask(z, b2), four_, d); // d = z > b2? d : 4
z = _mm512_max_epi8(z, b2);
z = _mm512_min_epi8(z, sc_mch_);
// __dp_code_block2_pcl;
__mmask64 msk;
{
// __mmask64 msk;
int ind = (en0 - t*64 + 16)/16;
msk = msk_ar2[ind];
off_end[r] -= (4-ind)*16;
_mm512_mask_storeu_epi8(&u[t], msk, _mm512_sub_epi8(z, vt1));
_mm512_mask_storeu_epi8(&v[t], msk, _mm512_sub_epi8(z, ut));
tmp = _mm512_sub_epi8(z, q_);
a = _mm512_sub_epi8(a, tmp);
b = _mm512_sub_epi8(b, tmp);
tmp = _mm512_sub_epi8(z, q2_);
a2= _mm512_sub_epi8(a2, tmp);
b2= _mm512_sub_epi8(b2, tmp);
}
{
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, a);
_mm512_mask_storeu_epi8(&x[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, a, zero_), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, s1_, zero_)); // d = a > 0? 1<<3 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, b);
_mm512_mask_storeu_epi8(&y[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, b, zero_), qe_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, s2_, zero_)); // d = b > 0? 1<<4 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, a2);
_mm512_mask_storeu_epi8(&x2[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, a2, zero_), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, s3_, zero_)); // d = a > 0? 1<<5 : 0
tmp_mask = _mm512_cmpgt_epi8_mask(zero_, b2);
_mm512_mask_storeu_epi8(&y2[t], msk, _mm512_sub_epi8(_mm512_mask_blend_epi8(tmp_mask, b2, zero_), qe2_));
d = _mm512_or_si512(d, _mm512_mask_blend_epi8(tmp_mask, s4_, zero_)); // d = b > 0? 1<<6 : 0
// _mm512_store_si512(&pr[t], d);
_mm512_mask_storeu_epi8(&pr[t], msk, d);
}
}
}
if (!approx_max) { // find the exact max with a 32-bit score array
int32_t max_H, max_t;
// compute H[], max_H and max_t
if (r > 0) {
int32_t HH[16], tt[16], en1 = st0 + (en0 - st0) / 16 * 16, i;
__m512i max_H_, max_t_;
max_H = H[en0] = en0 > 0? H[en0-1] + u8[en0] : H[en0] + v8[en0]; // special casing the last element
max_t = en0;
max_H_ = _mm512_set1_epi32(max_H);
max_t_ = _mm512_set1_epi32(max_t);
for (t = st0; t < en1; t += /*4*/16) { // this implements: H[t]+=v8[t]-qe; if(H[t]>max_H) max_H=H[t],max_t=t;
__m512i H1, tmp, t_;
__mmask16 tmp_mask;
H1 = _mm512_loadu_si512((__m512i*)&H[t]);
__m128i t__ = _mm_load_si128((__m128i*) &v8[t]);
t_ = _mm512_cvtepi8_epi32(t__);
H1 = _mm512_add_epi32(H1, t_);
_mm512_storeu_si512((__m512i*)&H[t], H1);
// making it 4 lanes to match accuracy
__m512i shfH, shft, max1, max2;
t_ = _mm512_set1_epi32(t);
t_ = _mm512_add_epi32(t_, bt32_);
shfH = _mm512_shuffle_i32x4(H1, H1, 0x31);
shft = _mm512_shuffle_i32x4(t_, t_, 0x31);
tmp_mask = _mm512_cmpgt_epi32_mask(shfH, H1);
max1 = _mm512_mask_blend_epi32(tmp_mask, H1, shfH);
max2 = _mm512_mask_blend_epi32(tmp_mask, t_, shft);
shfH = _mm512_shuffle_i32x4(max1, max1, 0x2);
shft = _mm512_shuffle_i32x4(max2, max2, 0x2);
tmp_mask = _mm512_cmpgt_epi32_mask(shfH, max1);
max1 = _mm512_mask_blend_epi32(tmp_mask, max1, shfH);
max2 = _mm512_mask_blend_epi32(tmp_mask, max2, shft);
tmp_mask = _mm512_cmpgt_epi32_mask(max1, max_H_);
max_H_ = _mm512_mask_blend_epi32(tmp_mask, max_H_, max1);
max_t_ = _mm512_mask_blend_epi32(tmp_mask, max_t_, max2);
}
_mm512_storeu_si512((__m512i*)HH, max_H_);
_mm512_storeu_si512((__m512i*)tt, max_t_);
int rem = (en0 - t) / 4;
for (int l=0; l<rem; l++) {
int bt = t;
for (int j=0; j<4; j++) {
H[t] += (int32_t)v8[t];
if (H[t] > HH[j]) {
HH[j] = H[t];
tt[j] = bt;
}
t++;
}
}
for (i = 0; i < 4; ++i)
if (max_H < HH[i]) max_H = HH[i], max_t = tt[i] + i;
for (; t < en0; ++t) { // for the rest of values that haven't been computed with SSE
H[t] += (int32_t)v8[t];
if (H[t] > max_H) {
max_H = H[t], max_t = t;
}
}
} else H[0] = v8[0] - qe, max_H = H[0], max_t = 0; // special casing r==0
// update ez
if (en0 == tlen - 1 && H[en0] > ez->mte) {
ez->mte = H[en0], ez->mte_q = r - en_new;
}
if (r - st0 == qlen - 1 && H[st0] > ez->mqe) {
ez->mqe = H[st0], ez->mqe_t = st0;
}
if (ksw_apply_zdrop(ez, 1, max_H, r, max_t, zdrop, e2)) {
break;
}
if (r == qlen + tlen - 2 && en0 == tlen - 1) {
ez->score = H[tlen - 1];
}
} else { // find approximate max; Z-drop might be inaccurate, too.
if (r > 0) {
if (last_H0_t >= st0 && last_H0_t <= en0 && last_H0_t + 1 >= st0 && last_H0_t + 1 <= en0) {
int32_t d0 = v8[last_H0_t];
int32_t d1 = u8[last_H0_t + 1];
if (d0 > d1) H0 += d0;
else H0 += d1, ++last_H0_t;
} else if (last_H0_t >= st0 && last_H0_t <= en0) {
H0 += v8[last_H0_t];
} else {
++last_H0_t, H0 += u8[last_H0_t];
}
} else H0 = v8[0] - qe, last_H0_t = 0;
if ((flag & KSW_EZ_APPROX_DROP) && ksw_apply_zdrop(ez, 1, H0, r, last_H0_t, zdrop, e2)) {
break;
}
if (r == qlen + tlen - 2 && en0 == tlen - 1) {
ez->score = H0;
}
}
// last_st = st, last_en = en;
last_st = st_new, last_en = en_new;
}
kfree(km, mem);
if (!approx_max) kfree(km, H);
if (with_cigar) { // backtrack
int rev_cigar = !!(flag & KSW_EZ_REV_CIGAR);
if (!ez->zdropped && !(flag&KSW_EZ_EXTZ_ONLY)) {
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*64, tlen-1, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
} else if (!ez->zdropped && (flag&KSW_EZ_EXTZ_ONLY) && ez->mqe + end_bonus > (int)ez->max) {
ez->reach_end = 1;
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*64, ez->mqe_t, qlen-1, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
} else if (ez->max_t >= 0 && ez->max_q >= 0) {
ksw_backtrack(km, 1, rev_cigar, 0, (uint8_t*)p, off, off_end, n_col_*64, ez->max_t, ez->max_q, &ez->m_cigar, &ez->n_cigar, &ez->cigar);
}
kfree(km, mem2); kfree(km, off);
}
}
#endif

40
ksw2_extd2_avx.h Normal file
View File

@@ -0,0 +1,40 @@
/* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2017-2018 Broad Institute, Inc.
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Modified Copyright (C) 2021 Intel Corporation
Contacts: Saurabh Kalikar <saurabh.kalikar@intel.com>;
Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
Chirag Jain <chirag@iisc.ac.in>; Heng Li <hli@jimmy.harvard.edu>
*/
#include <string.h>
#include <stdio.h>
#include <assert.h>
#include "ksw2.h"
#include <immintrin.h>
#include <x86intrin.h>
#include <smmintrin.h>
#include <emmintrin.h>
void ksw_extd2_avx512(void *km, int qlen, const uint8_t *query, int tlen, const uint8_t *target, int8_t m, const int8_t *mat,
int8_t q, int8_t e, int8_t q2, int8_t e2, int w, int zdrop, int end_bonus, int flag, ksw_extz_t *ez);

82
main.c
View File

@@ -1,13 +1,54 @@
/* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2017-2018 Broad Institute, Inc.
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Modified Copyright (C) 2021 Intel Corporation
Contacts: Saurabh Kalikar <saurabh.kalikar@intel.com>;
Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
Chirag Jain <chirag@iisc.ac.in>; Heng Li <hli@jimmy.harvard.edu>
*/
#include <stdlib.h>
#include <stdio.h>
#include <string.h>
#include <string>
#include <errno.h>
#include "bseq.h"
#include "minimap.h"
#include "mmpriv.h"
#include "ketopt.h"
#include <x86intrin.h>
#define MM_VERSION "2.18-r1015"
using namespace std;
#ifdef MANUAL_PROFILING
uint64_t num_reads = 0, minimizer_hit_time = 0, dp_chaining_time = 0, alignment_time = 0;
#endif
#ifdef LISA_HASH
#include "lisa_hash.h"
lisa_hash<uint64_t, uint64_t> *lh;
#endif
#ifdef __linux__
#include <sys/resource.h>
@@ -108,11 +149,12 @@ static inline void yes_or_no(mm_mapopt_t *opt, int flag, int long_idx, const cha
int main(int argc, char *argv[])
{
const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYPo:";
const char *opt_str = "2aSDw:k:K:t:r:f:Vv:g:G:I:d:XT:s:x:Hcp:M:n:z:A:B:O:E:m:N:Qu:R:hF:LC:yYPo:Z:";
ketopt_t o = KETOPT_INIT;
mm_mapopt_t opt;
mm_idxopt_t ipt;
int i, c, n_threads = 3, n_parts, old_best_n = -1;
uint64_t total_time = 0;
char *fnw = 0, *rg = 0, *junc_bed = 0, *s, *alt_list = 0;
FILE *fp_help = stderr;
mm_idx_reader_t *idx_rdr;
@@ -122,9 +164,11 @@ int main(int argc, char *argv[])
liftrlimit();
mm_realtime0 = realtime();
mm_set_opt(0, &ipt, &opt);
string preset_arg = "";
while ((c = ketopt(&o, argc, argv, 1, opt_str, long_options)) >= 0) { // test command line options and apply option -x/preset first
if (c == 'x') {
preset_arg += (string) o.arg;
if (mm_set_opt(o.arg, &ipt, &opt) < 0) {
fprintf(stderr, "[ERROR] unknown preset '%s'\n", o.arg);
return 1;
@@ -141,6 +185,7 @@ int main(int argc, char *argv[])
while ((c = ketopt(&o, argc, argv, 1, opt_str, long_options)) >= 0) {
if (c == 'w') ipt.w = atoi(o.arg);
else if (c == 'Z') opt.L_hash = atoi(o.arg);
else if (c == 'k') ipt.k = atoi(o.arg);
else if (c == 'H') ipt.flag |= MM_I_HPC;
else if (c == 'd') fnw = o.arg; // the above are indexing related options, except -I
@@ -345,7 +390,12 @@ int main(int argc, char *argv[])
fprintf(stderr, "[ERROR] incorrect input: in the sr mode, please specify no more than two query files.\n");
return 1;
}
preset_arg = (string)argv[o.ind] + "_" + preset_arg + "_minimizers_key_value_sorted";
idx_rdr = mm_idx_reader_open(argv[o.ind], &ipt, fnw);
total_time = __rdtsc();
if (idx_rdr == 0) {
fprintf(stderr, "[ERROR] failed to open file '%s': %s\n", argv[o.ind], strerror(errno));
return 1;
@@ -387,9 +437,23 @@ int main(int argc, char *argv[])
__func__, realtime() - mm_realtime0, cputime() / (realtime() - mm_realtime0), mi->n_seq);
if (argc != o.ind + 1) mm_mapopt_update(&opt, mi);
if (mm_verbose >= 3) mm_idx_stat(mi);
if(opt.L_hash == 1) {
fprintf(stderr, "Generating lisa-hash..\n");
mm_idx_dump_hash(preset_arg.c_str(), mi);
fprintf(stderr, "Lisa-hash saving done.. \n");
exit(0);
}
if (junc_bed) mm_idx_bed_read(mi, junc_bed, 1);
if (alt_list) mm_idx_alt_read(mi, alt_list);
ret = 0;
#ifdef LISA_HASH
fprintf(stderr, "Using LISA_HASH..\n");
mm_idx_destroy_mm_hash(mi);
char* prefix;
lh = new lisa_hash<uint64_t, uint64_t>(preset_arg, prefix);
fprintf(stderr, "Loading done.\n");
total_time = __rdtsc();
#endif
if (!(opt.flag & MM_F_FRAG_MODE)) {
for (i = o.ind + 1; i < argc; ++i) {
ret = mm_map_file(mi, argv[i], &opt, n_threads);
@@ -398,11 +462,15 @@ int main(int argc, char *argv[])
} else {
ret = mm_map_file_frag(mi, argc - (o.ind + 1), (const char**)&argv[o.ind + 1], &opt, n_threads);
}
mm_idx_destroy(mi);
if (ret < 0) {
fprintf(stderr, "ERROR: failed to map the query file\n");
exit(EXIT_FAILURE);
}
#ifdef LISA_HASH
mm_idx_destroy_seq(mi);
#else
mm_idx_destroy(mi);
#endif
}
n_parts = idx_rdr->n_parts;
mm_idx_reader_close(idx_rdr);
@@ -422,5 +490,13 @@ int main(int argc, char *argv[])
fprintf(stderr, " %s", argv[i]);
fprintf(stderr, "\n[M::%s] Real time: %.3f sec; CPU: %.3f sec; Peak RSS: %.3f GB\n", __func__, realtime() - mm_realtime0, cputime(), peakrss() / 1024.0 / 1024.0 / 1024.0);
}
return 0;
#ifdef MANUAL_PROFILING
fprintf(stderr, "\n Number of reads = %lld Minimizer hit time = %lld dp_chaining time = %lld alignment time = %lld total time = %lld \n", num_reads, minimizer_hit_time, dp_chaining_time, alignment_time, __rdtsc() - total_time);
#endif
fprintf(stderr, "Total ticks: %lld \n",__rdtsc() - total_time);
#ifdef LISA_HASH
delete lh;
#endif
return 0;
}

221
map.c
View File

@@ -1,3 +1,32 @@
/* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2017-2018 Broad Institute, Inc.
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Modified Copyright (C) 2021 Intel Corporation
Contacts: Saurabh Kalikar <saurabh.kalikar@intel.com>;
Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
Chirag Jain <chirag@iisc.ac.in>; Heng Li <hli@jimmy.harvard.edu>
*/
#include <stdlib.h>
#include <string.h>
#include <assert.h>
@@ -9,6 +38,17 @@
#include "mmpriv.h"
#include "bseq.h"
#include "khash.h"
#include <x86intrin.h>
#ifdef LISA_HASH
#include "lisa_hash.h"
extern lisa_hash<uint64_t, uint64_t> *lh;
#endif
#ifdef MANUAL_PROFILING
extern uint64_t num_reads, minimizer_hit_time, dp_chaining_time, alignment_time;
#endif
struct mm_tbuf_s {
void *km;
@@ -87,6 +127,77 @@ typedef struct {
const uint64_t *cr;
} mm_match_t;
#ifdef LISA_HASH
static mm_match_t *collect_matches_lisa_hash(void *km, int *_n_m, int max_occ, const mm_idx_t *mi, const mm128_v *mv, int64_t *n_a, int *rep_len, int *n_mini_pos, uint64_t **mini_pos)
{
uint64_t** cr_batch = (uint64_t**) malloc((mv->n)*sizeof(uint64_t*));
int* t_batch = (int*)malloc((mv->n)*sizeof(int));
uint64_t* minimizers = (uint64_t*) malloc((mv->n)*sizeof(uint64_t));
int64_t* lisa_pos = (int64_t*) malloc((max(32, (int)mv->n))* sizeof(int64_t));
int rep_st = 0, rep_en = 0, n_m;
size_t i;
mm_match_t *m;
*n_mini_pos = 0;
*mini_pos = (uint64_t*)kmalloc(km, mv->n * sizeof(uint64_t));
m = (mm_match_t*)kmalloc(km, mv->n * sizeof(mm_match_t));
for (i = 0; i < mv->n; i++) {
mm128_t *p = &mv->a[i];
minimizers[i] = p->x>>8;
}
lh->mm_idx_get_batched(minimizers, mv->n, lisa_pos, cr_batch, t_batch);
for (i = 0, n_m = 0, *rep_len = 0, *n_a = 0; i < mv->n; ++i) {
const uint64_t *cr;
mm128_t *p = &mv->a[i];
uint32_t q_pos = (uint32_t)p->y, q_span = p->x & 0xff;
int t;
cr = cr_batch[i]; t = t_batch[i];
/*Correctness check for lisa_hash*/
#ifdef LISA_HASH_ASSERT
int t_minimap2_original;
const uint64_t *cr_minimap2_hash = mm_idx_get(mi, p->x>>8, &t);
cr_minimap2_hash = mm_idx_get(mi, p->x>>8, &t_minimap2_original);
assert(t == t_minimap2_original);
#endif
if (t >= max_occ) {
int en = (q_pos >> 1) + 1, st = en - q_span;
if (st > rep_en) {
*rep_len += rep_en - rep_st;
rep_st = st, rep_en = en;
} else rep_en = en;
} else {
#ifdef LISA_HASH_ASSERT
//Correctness assertion
for(int itr = 0; itr < t; itr++){
assert((cr[itr] == cr_minimap2_hash[itr]));
}
#endif
mm_match_t *q = &m[n_m++];
q->q_pos = q_pos, q->q_span = q_span, q->cr = cr, q->n = t, q->seg_id = p->y >> 32;
q->is_tandem = 0;
if (i > 0 && p->x>>8 == mv->a[i - 1].x>>8) q->is_tandem = 1;
if (i < mv->n - 1 && p->x>>8 == mv->a[i + 1].x>>8) q->is_tandem = 1;
*n_a += q->n;
(*mini_pos)[(*n_mini_pos)++] = (uint64_t)q_span<<32 | q_pos>>1;
}
}
free(cr_batch);
free(t_batch);
free(minimizers);
free(lisa_pos);
*rep_len += rep_en - rep_st;
*_n_m = n_m;
return m;
}
#endif
static mm_match_t *collect_matches(void *km, int *_n_m, int max_occ, const mm_idx_t *mi, const mm128_v *mv, int64_t *n_a, int *rep_len, int *n_mini_pos, uint64_t **mini_pos)
{
int rep_st = 0, rep_en = 0, n_m;
@@ -146,6 +257,51 @@ static inline int skip_seed(int flag, uint64_t r, const mm_match_t *q, const cha
return 0;
}
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 i, n_m;
mm_match_t *m;
mm128_t *a;
#ifndef LISA_HASH
m = collect_matches(km, &n_m, max_occ, mi, mv, n_a, rep_len, n_mini_pos, mini_pos);
#else
m = collect_matches_lisa_hash(km, &n_m, max_occ, mi, mv, n_a, rep_len, n_mini_pos, mini_pos);
#endif
uint64_t mapping_count = 0;
mapping_count = 0;
a = (mm128_t*)kmalloc(km, *n_a * sizeof(mm128_t));
for (i = 0, *n_a = 0; i < n_m; ++i) {
mm_match_t *q = &m[i];
const uint64_t *r = q->cr;
uint32_t k;
for (k = 0; k < q->n; ++k) {
uint64_t r_k = r[k];
int32_t is_self, rpos = (uint32_t)r_k >> 1;
mm128_t *p;
if (skip_seed(opt->flag, r_k, q, qname, qlen, mi, &is_self)) continue;
p = &a[(*n_a)++];
if ((r_k&1) == (q->q_pos&1)) { // forward strand
p->x = (r_k & 0xffffffff00000000ULL) | rpos;
p->y = (uint64_t)q->q_span << 32 | q->q_pos >> 1;
} else { // reverse strand
p->x = 1ULL<<63 | (r_k & 0xffffffff00000000ULL) | rpos;
p->y = (uint64_t)q->q_span << 32 | (qlen - ((q->q_pos>>1) + 1 - q->q_span) - 1);
}
p->y |= (uint64_t)q->seg_id << MM_SEED_SEG_SHIFT;
if (q->is_tandem) p->y |= MM_SEED_TANDEM;
if (is_self) p->y |= MM_SEED_SELF;
}
}
kfree(km, m);
radix_sort_128x(a, a + (*n_a));
return a;
}
static mm128_t *collect_seed_hits_heap(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)
{
@@ -212,40 +368,6 @@ static mm128_t *collect_seed_hits_heap(void *km, const mm_mapopt_t *opt, int max
return a;
}
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 i, n_m;
mm_match_t *m;
mm128_t *a;
m = collect_matches(km, &n_m, max_occ, mi, mv, n_a, rep_len, n_mini_pos, mini_pos);
a = (mm128_t*)kmalloc(km, *n_a * sizeof(mm128_t));
for (i = 0, *n_a = 0; i < n_m; ++i) {
mm_match_t *q = &m[i];
const uint64_t *r = q->cr;
uint32_t k;
for (k = 0; k < q->n; ++k) {
int32_t is_self, rpos = (uint32_t)r[k] >> 1;
mm128_t *p;
if (skip_seed(opt->flag, r[k], q, qname, qlen, mi, &is_self)) continue;
p = &a[(*n_a)++];
if ((r[k]&1) == (q->q_pos&1)) { // forward strand
p->x = (r[k]&0xffffffff00000000ULL) | rpos;
p->y = (uint64_t)q->q_span << 32 | q->q_pos >> 1;
} else { // reverse strand
p->x = 1ULL<<63 | (r[k]&0xffffffff00000000ULL) | rpos;
p->y = (uint64_t)q->q_span << 32 | (qlen - ((q->q_pos>>1) + 1 - q->q_span) - 1);
}
p->y |= (uint64_t)q->seg_id << MM_SEED_SEG_SHIFT;
if (q->is_tandem) p->y |= MM_SEED_TANDEM;
if (is_self) p->y |= MM_SEED_SELF;
}
}
kfree(km, m);
radix_sort_128x(a, a + (*n_a));
return a;
}
static void chain_post(const mm_mapopt_t *opt, int max_chain_gap_ref, const mm_idx_t *mi, void *km, int qlen, int n_segs, const int *qlens, int *n_regs, mm_reg1_t *regs, mm128_t *a)
{
if (!(opt->flag & MM_F_ALL_CHAINS)) { // don't choose primary mapping(s)
@@ -271,6 +393,11 @@ static mm_reg1_t *align_regs(const mm_mapopt_t *opt, const mm_idx_t *mi, void *k
void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **seqs, int *n_regs, mm_reg1_t **regs, mm_tbuf_t *b, const mm_mapopt_t *opt, const char *qname)
{
#ifdef MANUAL_PROFILING
num_reads++;
#endif
int i, j, rep_len, qlen_sum, n_regs0, n_mini_pos;
int max_chain_gap_qry, max_chain_gap_ref, is_splice = !!(opt->flag & MM_F_SPLICE), is_sr = !!(opt->flag & MM_F_SR);
uint32_t hash;
@@ -293,8 +420,18 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
collect_minimizers(b->km, opt, mi, n_segs, qlens, seqs, &mv);
if (opt->flag & MM_F_HEAP_SORT) a = collect_seed_hits_heap(b->km, opt, opt->mid_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
else a = collect_seed_hits(b->km, opt, opt->mid_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
else {
#ifdef MANUAL_PROFILING
uint64_t mm_hit_start = __rdtsc();
#endif
a = collect_seed_hits(b->km, opt, opt->mid_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
#ifdef MANUAL_PROFILING
minimizer_hit_time += (__rdtsc() - mm_hit_start);
#endif
}
if (mm_dbg_flag & MM_DBG_PRINT_SEED) {
fprintf(stderr, "RS\t%d\n", rep_len);
for (i = 0; i < n_a; ++i)
@@ -312,9 +449,16 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
max_chain_gap_ref = opt->max_frag_len - qlen_sum;
if (max_chain_gap_ref < opt->max_gap) max_chain_gap_ref = opt->max_gap;
} else max_chain_gap_ref = opt->max_gap;
#ifdef MANUAL_PROFILING
uint64_t dp_start = __rdtsc();
#endif
a = mm_chain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->max_chain_iter, opt->min_cnt, opt->min_chain_score, opt->chain_gap_scale, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
#ifdef MANUAL_PROFILING
dp_chaining_time += (__rdtsc() - dp_start);
#endif
if (opt->max_occ > opt->mid_occ && rep_len > 0) {
int rechain = 0;
if (n_regs0 > 0) { // test if the best chain has all the segments
@@ -335,6 +479,7 @@ void mm_map_frag(const mm_idx_t *mi, int n_segs, const int *qlens, const char **
kfree(b->km, mini_pos);
if (opt->flag & MM_F_HEAP_SORT) a = collect_seed_hits_heap(b->km, opt, opt->max_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
else a = collect_seed_hits(b->km, opt, opt->max_occ, mi, qname, &mv, qlen_sum, &n_a, &rep_len, &n_mini_pos, &mini_pos);
a = mm_chain_dp(max_chain_gap_ref, max_chain_gap_qry, opt->bw, opt->max_chain_skip, opt->max_chain_iter, opt->min_cnt, opt->min_chain_score, opt->chain_gap_scale, is_splice, n_segs, n_a, a, &n_regs0, &u, b->km);
}
}
@@ -430,6 +575,7 @@ static void worker_for(void *_data, long i, int tid) // kt_for() callback
int qlens[MM_MAX_SEG], j, off = s->seg_off[i], pe_ori = s->p->opt->pe_ori;
const char *qseqs[MM_MAX_SEG];
mm_tbuf_t *b = s->buf[tid];
assert(s->n_seg[i] <= MM_MAX_SEG);
if (mm_dbg_flag & MM_DBG_PRINT_QNAME)
fprintf(stderr, "QR\t%s\t%d\t%d\n", s->seq[off].name, tid, s->seq[off].l_seq);
@@ -561,6 +707,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
else kt_for(p->n_threads, worker_for, in, ((step_t*)in)->n_frag);
return in;
} else if (step == 2) { // step 2: output
void *km = 0;
step_t *s = (step_t*)in;
const mm_idx_t *mi = p->mi;
@@ -569,6 +716,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
if ((p->opt->flag & MM_F_OUT_CS) && !(mm_dbg_flag & MM_DBG_NO_KALLOC)) km = km_init();
for (k = 0; k < s->n_frag; ++k) {
int seg_st = s->seg_off[k], seg_en = s->seg_off[k] + s->n_seg[k];
#ifndef DISABLE_OUTPUT
for (i = seg_st; i < seg_en; ++i) {
mm_bseq1_t *t = &s->seq[i];
if (p->opt->split_prefix && p->n_parts == 0) { // then write to temporary files
@@ -603,6 +751,7 @@ static void *worker_pipeline(void *shared, int step, void *in)
mm_err_puts(p->str.s);
}
}
#endif
for (i = seg_st; i < seg_en; ++i) {
for (j = 0; j < s->n_reg[i]; ++j) free(s->reg[i][j].p);
free(s->reg[i]);

54
minimap.h
View File

@@ -1,3 +1,32 @@
/* The MIT License
Copyright (c) 2018- Dana-Farber Cancer Institute
2017-2018 Broad Institute, Inc.
Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions:
The above copyright notice and this permission notice shall be
included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
Modified Copyright (C) 2021 Intel Corporation
Contacts: Saurabh Kalikar <saurabh.kalikar@intel.com>;
Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
Chirag Jain <chirag@iisc.ac.in>; Heng Li <hli@jimmy.harvard.edu>
*/
#ifndef MINIMAP2_H
#define MINIMAP2_H
@@ -153,6 +182,8 @@ typedef struct {
int64_t max_sw_mat;
const char *split_prefix;
// Store minimizer hash to a file as key and list of values
int L_hash;
} mm_mapopt_t;
// index reader
@@ -267,6 +298,14 @@ mm_idx_t *mm_idx_load(FILE *fp);
*/
void mm_idx_dump(FILE *fp, const mm_idx_t *mi);
/**
* Store hash table from minimap2 index into a file
* @param f_name File name for output file
* @param mi minimap2 index
*/
void mm_idx_dump_hash(const char* f_name, const mm_idx_t *mi);
/**
* Create an index from strings in memory
*
@@ -296,6 +335,21 @@ void mm_idx_stat(const mm_idx_t *idx);
*/
void mm_idx_destroy(mm_idx_t *mi);
/**
* Destroy/deallocate an hash table index
*
* @param r minimap2 index
*/
void mm_idx_destroy_mm_hash(mm_idx_t *mi);
/**
* Destroy/deallocate target sequences
*
* @param r minimap2 index
*/
void mm_idx_destroy_seq(mm_idx_t *mi);
/**
* Initialize a thread-local buffer for mapping
*