repo stringlengths 1 152 ⌀ | file stringlengths 14 221 | code stringlengths 501 25k | file_length int64 501 25k | avg_line_length float64 20 99.5 | max_line_length int64 21 134 | extension_type stringclasses 2
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|---|---|---|---|---|---|---|
kotekan | kotekan-master/lib/utils/nt_memcpy.c | #include "nt_memcpy.h"
#include <assert.h> // for assert
#include <emmintrin.h> // for __m128i, _mm_stream_si128, _mm_load_si128, _mm_loadu_si128
#include <stdint.h> // for uintptr_t
#include <stdlib.h> // for size_t
#include <xmmintrin.h> // for _MM_HINT_NTA, _mm_prefetch
#ifdef __AVX__
// Assumes that the ... | 3,798 | 36.613861 | 88 | c |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/alignment.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 10,038 | 24.544529 | 107 | c |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/db_alignment.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 6,252 | 25.383966 | 117 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/threadpool.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 1,756 | 27.33871 | 89 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/score_database_gpu_long.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 2,365 | 37.16129 | 111 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/thread.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 5,357 | 22.39738 | 100 | c |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/sse_module.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 2,028 | 33.982759 | 106 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/cpu_module.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 6,290 | 38.566038 | 107 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/scorer.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 5,727 | 25.036364 | 89 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/database.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 7,660 | 43.80117 | 108 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/swsharp.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 3,014 | 23.314516 | 89 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/evalue.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 1,628 | 30.326923 | 89 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/utils.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 3,492 | 32.912621 | 89 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/reconstruct.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 18,337 | 28.769481 | 92 | c |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/align.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 4,984 | 36.765152 | 99 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/pre_proc.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 19,428 | 22.493349 | 89 | c |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/constants.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 2,237 | 23.593407 | 89 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/chain.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 4,858 | 25.551913 | 89 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/sse_module.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 11,124 | 23.450549 | 105 | c |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/scorer.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This pro... | 10,734 | 26.246193 | 89 | c |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/gpu_module.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 14,030 | 45.003279 | 106 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/threadpool.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 7,811 | 22.459459 | 89 | c |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/db_alignment.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 6,524 | 28 | 113 | c |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/chain.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 7,506 | 22.756329 | 89 | c |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/post_proc.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 7,086 | 30.497778 | 104 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/error.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 3,410 | 43.298701 | 89 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/alignment.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 6,439 | 24.76 | 111 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/pre_proc.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 5,334 | 36.307692 | 90 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/score_database_gpu_short.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 3,084 | 41.847222 | 122 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/reconstruct.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 2,969 | 36.594937 | 95 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/cuda_utils.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 3,672 | 30.663793 | 116 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/ssw/ssw.h | /*
* ssw.h
*
* Created by Mengyao Zhao on 6/22/10.
* Copyright 2010 Boston College. All rights reserved.
* Version 0.1.4
* Last revision by Mengyao Zhao on 01/30/13.
*
*/
#ifndef SSW_H
#define SSW_H
#include <stdio.h>
#include <stdint.h>
#include <string.h>
#include <emmintrin.h>
/*! @typedef structure of... | 6,380 | 47.709924 | 128 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharp/src/swimd/Swimd.h | #ifndef SWIMD_H
#define SWIMD_H
/***********************************************************************************
* - adapts score type and reports overflow if score does not fit in int
* - calculating column by column (not 4 of them at once)
* - db sequences are not padded
* - using saturation arithmetic w... | 4,824 | 47.25 | 111 | h |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharpn/src/main.c | #include <getopt.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/time.h>
#define SYCL_LANGUAGE_VERSION 1
#include "swsharp/swsharp.h"
static FILE *fileSafeOpen(const char *path, const char *mode)
{
FILE *f = fopen(path, mode);
return f;
}
double dwalltime()
{
double sec;
struct ti... | 8,695 | 24.880952 | 83 | c |
swsharp_sycl | swsharp_sycl-master/CUDA/swsharpdb/src/main.c | #include <getopt.h>
#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <sys/time.h>
#define SYCL_LANGUAGE_VERSION 1
#include "swsharp/evalue.h"
#include "swsharp/swsharp.h"
static FILE *fileSafeOpen(const char *path, const char *mode)
{
FILE *f = fopen(path, mode);
return f;
}
double dwalltime()... | 13,912 | 25.551527 | 83 | c |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/alignment.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 10,038 | 24.544529 | 107 | c |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/db_alignment.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 6,252 | 25.383966 | 117 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/threadpool.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 1,756 | 27.33871 | 89 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/score_database_gpu_long.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 2,365 | 37.16129 | 111 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/thread.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 5,357 | 22.39738 | 100 | c |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/sse_module.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 2,028 | 33.982759 | 106 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/cpu_module.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 6,290 | 38.566038 | 107 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/scorer.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 5,727 | 25.036364 | 89 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/database.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 7,660 | 43.80117 | 108 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/swsharp.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 3,014 | 23.314516 | 89 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/evalue.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 1,628 | 30.326923 | 89 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/utils.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 3,492 | 32.912621 | 89 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/reconstruct.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 18,337 | 28.769481 | 92 | c |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/align.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 4,984 | 36.765152 | 99 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/pre_proc.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 19,428 | 22.493349 | 89 | c |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/constants.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 2,237 | 23.593407 | 89 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/chain.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 4,858 | 25.551913 | 89 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/sse_module.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 11,124 | 23.450549 | 105 | c |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/scorer.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This pro... | 10,734 | 26.246193 | 89 | c |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/gpu_module.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 14,030 | 45.003279 | 106 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/threadpool.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 7,811 | 22.389222 | 89 | c |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/db_alignment.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This prog... | 6,420 | 30.169903 | 89 | c |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/chain.c | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 7,506 | 22.756329 | 89 | c |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/post_proc.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 7,086 | 30.497778 | 104 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/error.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 3,410 | 43.298701 | 89 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/alignment.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 6,439 | 24.76 | 111 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/pre_proc.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 5,334 | 36.307692 | 90 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/score_database_gpu_short.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 3,084 | 41.847222 | 122 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/reconstruct.h | /*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This progr... | 2,969 | 36.594937 | 95 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/cuda_utils.h |
#ifdef SYCL_LANGUAGE_VERSION
#include <CL/sycl.hpp>
#ifdef HIP
namespace sycl = cl::sycl;
#endif
/*
This code represents a SYCL-compatible, DPC++-based version of SW#.
Copyright (C) 2022 Manuel Costanzo, contributor Enzo Rucci.
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algori... | 3,072 | 25.95614 | 114 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/ssw/ssw.h | /*
* ssw.h
*
* Created by Mengyao Zhao on 6/22/10.
* Copyright 2010 Boston College. All rights reserved.
* Version 0.1.4
* Last revision by Mengyao Zhao on 01/30/13.
*
*/
#ifndef SSW_H
#define SSW_H
#include <stdio.h>
#include <stdint.h>
#include <string.h>
#include <emmintrin.h>
/*! @typedef structure of... | 6,380 | 47.709924 | 128 | h |
swsharp_sycl | swsharp_sycl-master/SYCL/swsharp/src/swimd/Swimd.h | #ifndef SWIMD_H
#define SWIMD_H
/***********************************************************************************
* - adapts score type and reports overflow if score does not fit in int
* - calculating column by column (not 4 of them at once)
* - db sequences are not padded
* - using saturation arithmetic w... | 4,824 | 47.25 | 111 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/utils.c | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 6,902 | 21.707237 | 84 | c |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/alignment.c | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 9,920 | 26.032698 | 83 | c |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/db_alignment.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 5,459 | 22.636364 | 81 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/threadpool.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 1,494 | 26.685185 | 85 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/score_database_gpu_long.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 1,912 | 33.160714 | 81 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/thread.c | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 5,150 | 23.528571 | 101 | c |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/sse_module.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 1,652 | 30.788462 | 77 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/cpu_module.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 5,551 | 35.287582 | 81 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/scorer.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 5,023 | 22.476636 | 80 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/database.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 6,793 | 40.175758 | 81 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/swsharp.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 2,836 | 23.042373 | 82 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/evalue.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 1,357 | 28.521739 | 74 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/utils.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 2,391 | 24.72043 | 85 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/reconstruct.c | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 18,323 | 30.538726 | 92 | c |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/align.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 4,377 | 33.746032 | 81 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/pre_proc.c | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 18,466 | 24.436639 | 86 | c |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/constants.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 2,009 | 22.647059 | 74 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/chain.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 4,460 | 24.20339 | 81 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/sse_module.c | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 10,304 | 24.31941 | 86 | c |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/scorer.c | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published b... | 11,107 | 29.432877 | 82 | c |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/gpu_module.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 12,634 | 41.257525 | 83 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/threadpool.c | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 7,524 | 25.038062 | 86 | c |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/db_alignment.c | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 6,200 | 29.850746 | 81 | c |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/chain.c | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 7,315 | 24.58042 | 81 | c |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/post_proc.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 6,448 | 28.447489 | 98 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/error.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 1,799 | 26.692308 | 76 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/alignment.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 5,684 | 22.29918 | 82 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/pre_proc.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 4,705 | 33.350365 | 80 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/score_database_gpu_short.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 2,398 | 35.348485 | 80 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/reconstruct.h | /*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
... | 2,583 | 34.39726 | 80 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/cuda_utils.h |
#ifdef SYCL_LANGUAGE_VERSION
#include <CL/sycl.hpp>
#include <dpct/dpct.hpp>
/*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić
This program is free software: you can redistribute it and/or... | 2,983 | 25.40708 | 77 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/ssw/ssw.h | /*
* ssw.h
*
* Created by Mengyao Zhao on 6/22/10.
* Copyright 2010 Boston College. All rights reserved.
* Version 0.1.4
* Last revision by Mengyao Zhao on 01/30/13.
*
*/
#ifndef SSW_H
#define SSW_H
#include <stdio.h>
#include <stdint.h>
#include <string.h>
#include <emmintrin.h>
/*! @typedef structure of... | 6,380 | 47.709924 | 128 | h |
swsharp_sycl | swsharp_sycl-master/dpct_original_output/src/swimd/Swimd.h | #ifndef SWIMD_H
#define SWIMD_H
/***********************************************************************************
* - adapts score type and reports overflow if score does not fit in int
* - calculating column by column (not 4 of them at once)
* - db sequences are not padded
* - using saturation arithmetic w... | 4,824 | 47.25 | 111 | h |
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