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///////////////////////////////////////////////////////////////////////////////////// | |
// Compare HMMs with one another and look for sub-optimal alignments that share no pair with previous ones | |
// The function is called with q and t | |
// If q and t are equal (self==1), only the upper right part of the matrix is calculated: j>=i+3 | |
///////////////////////////////////////////////////////////////////////////////////// | |
void Hit::Viterbi(HMM* q, HMM* t, float** Sstruc) | |
{ | |
// Linear topology of query (and template) HMM: | |
// 1. The HMM HMM has L+2 columns. Columns 1 to L contain |
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#!/bin/bash -e | |
export CC=gcc | |
export CXX=g++ | |
cat <<'CPUDOC' | $CC -std=gnu99 -o "testcpu" -xc - | |
#include <stdio.h> | |
#define D(x) __builtin_cpu_supports((x))?(x) | |
int main(){puts(D("avx2"):D("sse4.1"):"fail");} | |
CPUDOC |
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{% set version = "2-23394" %} | |
{% set sha256 = "4734846e6fcc78a80058f1c699b2deb7f2a6b5c0cf1c1f1dd75a20403b81f387" %} | |
package: | |
name: mmseqs2 | |
version: {{ version }} | |
source: | |
fn: mmseqs2-{{ version }}.tar.gz | |
url: https://github.com/soedinglab/mmseqs2/archive/{{ version }}.tar.gz |
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Index: src/alignment/MsaFilter.cpp | |
IDEA additional info: | |
Subsystem: com.intellij.openapi.diff.impl.patch.CharsetEP | |
<+>UTF-8 | |
=================================================================== | |
--- src/alignment/MsaFilter.cpp (revision 2339462c06eab0bee64e4fc0ebebf7707f6e53fd) | |
+++ src/alignment/MsaFilter.cpp (date 1520402320000) | |
@@ -245,6 +245,13 @@ | |
<< ": " << __func__ << ":" << "\n"; | |
Debug(Debug::WARNING) |
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template <unsigned int N> __m256i _mm256_shift_left2(__m256i a) { | |
__m256i mask = _mm256_srli_si256( | |
_mm256_permute2x128_si256(a, a, _MM_SHUFFLE(0,0,3,0)) , 16-N); | |
return _mm256_or_si256(_mm256_slli_si256(a,N),mask); | |
} |
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inline float get_first( const __m128 vec){return _mm_cvtss_f32(_mm_shuffle_ps(vec,vec, _MM_SHUFFLE2(0,0)));} | |
inline float get_second(const __m128 vec){return _mm_cvtss_f32(_mm_shuffle_ps(vec,vec, _MM_SHUFFLE2(0,1)));} | |
inline float get_third( const __m128 vec){return _mm_cvtss_f32(_mm_shuffle_ps(vec,vec, _MM_SHUFFLE2(1,0)));} | |
inline float get_fourth(const __m128 vec){return _mm_cvtss_f32(_mm_shuffle_ps(vec,vec, _MM_SHUFFLE2(1,1)));} |