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/*
* The MIT License
*
* Wavefront Alignment Algorithms
* Copyright (c) 2017 by Santiago Marco-Sola <santiagomsola@gmail.com>
*
* This file is part of Wavefront Alignment Algorithms.
*
* 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.
*
* PROJECT: Wavefront Alignment Algorithms
* AUTHOR(S): Santiago Marco-Sola <santiagomsola@gmail.com>
*/
#include "align_benchmark_params.h"
/*
* Match function
*/
match_function_params_t match_function_params;
/*
* Default parameters
*/
align_bench_params_t parameters = {
// Algorithm
.algorithm = alignment_edit_wavefront,
// I/O
.input_filename = NULL,
.output_filename = NULL,
.output_full = false,
.output_file = NULL,
// I/O internals
.input_file = NULL,
.line1 = NULL,
.line2 = NULL,
.line1_allocated = 0,
.line2_allocated = 0,
// Penalties
.linear_penalties = {
.match = 0,
.mismatch = 4,
.indel = 2,
},
.affine_penalties = {
.match = 0,
.mismatch = 4,
.gap_opening = 6,
.gap_extension = 2,
},
.affine2p_penalties = {
.match = 0,
.mismatch = 4,
.gap_opening1 = 6,
.gap_extension1 = 2,
.gap_opening2 = 24,
.gap_extension2 = 1,
},
// Alignment form
.endsfree = false,
.pattern_begin_free = 0.0,
.text_begin_free = 0.0,
.pattern_end_free = 0.0,
.text_end_free = 0.0,
// Wavefront parameters
.wfa_score_only = false,
.wfa_heuristic = wf_heuristic_none,
.wfa_heuristic_p1 = -1,
.wfa_heuristic_p2 = -1,
.wfa_heuristic_p3 = -1,
.wfa_memory_mode = wavefront_memory_high,
.wfa_match_funct = NULL,
.wfa_match_funct_arguments = NULL,
.wfa_max_memory = UINT64_MAX,
.wfa_max_score = INT_MAX,
.wfa_max_threads = 1,
// Other algorithms parameters
.bandwidth = -1,
// Misc
.check_bandwidth = -1,
.check_display = false,
.check_correct = false,
.check_score = false,
.check_alignments = false,
.check_metric = ALIGN_DEBUG_CHECK_DISTANCE_METRIC_GAP_AFFINE,
.plot = 0,
// System
.num_threads = 1,
.batch_size = 10000,
.progress = 100000,
.verbose = 0,
};
/*
* Simplest Extend-matching function (for testing purposes)
*/
int match_function(int v,int h,void* arguments) {
// Extract parameters
match_function_params_t* match_arguments = (match_function_params_t*)arguments;
// Check match
if (v > match_arguments->pattern_length || h > match_arguments->text_length) return 0;
return (match_arguments->pattern[v] == match_arguments->text[h]);
}
/*
* Menu
*/
void usage() {
fprintf(stderr,
"USE: ./align_benchmark -a ALGORITHM -i PATH \n"
" Options:: \n"
" [Algorithm] \n"
" --algorithm|a ALGORITHM \n"
" [Indel (Longest Common Subsequence)] \n"
" indel-wfa \n"
" [Edit (Levenshtein)] \n"
" edit-bpm \n"
" edit-dp \n"
" edit-dp-banded \n"
" edit-wfa \n"
" [Gap-linear (Needleman-Wunsch)] \n"
" gap-linear-nw \n"
" gap-linear-wfa \n"
" [Gap-affine (Smith-Waterman-Gotoh)] \n"
" gap-affine-swg \n"
" gap-affine-swg-banded \n"
" gap-affine-wfa \n"
" [Gap-affine-2pieces (Concave 2-pieces)] \n"
" gap-affine2p-dp \n"
" gap-affine2p-wfa \n"
" [Input & Output] \n"
" --input|i PATH \n"
" --output|o PATH \n"
" --output-full PATH \n"
" [Penalties & Span] \n"
" --linear-penalties|p M,X,I \n"
" --affine-penalties|g M,X,O,E \n"
" --affine2p-penalties M,X,O1,E1,O2,E2 \n"
" --ends-free P0,Pf,T0,Tf \n"
" [Wavefront parameters] \n"
" --wfa-score-only \n"
" --wfa-memory-mode 'high'|'med'|'low'|'ultralow' \n"
" --wfa-heuristic STRATEGY \n"
" --wfa-heuristic-parameters P1,P2[,P3] \n"
" [STRATEGY='banded-static'] \n"
" P1 = minimum-diagonal-band (e.g., -100) \n"
" P2 = maximum-diagonal-band (e.g., +100) \n"
" [STRATEGY='banded-adaptive'] \n"
" P1 = minimum-diagonal-band (e.g., -100) \n"
" P2 = maximum-diagonal-band (e.g., +100) \n"
" P3 = steps-between-cutoffs \n"
" [STRATEGY='wfa-adaptive'] \n"
" P1 = minimum-wavefront-length \n"
" P2 = maximum-difference-distance \n"
" P3 = steps-between-cutoffs \n"
" [STRATEGY='xdrop'] \n"
" P1 = x-drop \n"
" P2 = steps-between-cutoffs \n"
" [STRATEGY='zdrop'] \n"
" P1 = z-drop \n"
" P2 = steps-between-cutoffs \n"
" --wfa-max-memory BYTES \n"
" --wfa-max-score INT \n"
" --wfa-max-threads INT (intra-parallelism; default=1) \n"
" [Other Parameters] \n"
" --bandwidth INT \n"
" [Misc] \n"
" --check|c 'correct'|'score'|'alignment' \n"
" --check-distance 'indel'|'edit'|'linear'|'affine'|'affine2p' \n"
" --check-bandwidth INT \n"
" --plot \n"
" [System] \n"
" --num-threads|t INT \n"
" --batch-size INT \n"
//" --progress|P INT \n"
" --verbose|v INT \n"
" --quiet|q \n"
" --help|h \n");
}
/*
* Parsing arguments
*/
void parse_arguments(
int argc,
char** argv) {
struct option long_options[] = {
/* Input */
{ "algorithm", required_argument, 0, 'a' },
{ "input", required_argument, 0, 'i' },
{ "output", required_argument, 0, 'o' },
{ "output-full", required_argument, 0, 800 },
/* Penalties */
{ "linear-penalties", required_argument, 0, 'p' },
{ "affine-penalties", required_argument, 0, 'g' },
{ "affine2p-penalties", required_argument, 0, 900 },
{ "ends-free", required_argument, 0, 901 },
/* Wavefront parameters */
{ "wfa-score-only", no_argument, 0, 1000 },
{ "wfa-memory-mode", required_argument, 0, 1001 },
{ "wfa-heuristic", required_argument, 0, 1002 },
{ "wfa-heuristic-parameters", required_argument, 0, 1003 },
{ "wfa-custom-match-funct", no_argument, 0, 1004 },
{ "wfa-max-memory", required_argument, 0, 1005 },
{ "wfa-max-score", required_argument, 0, 1006 },
{ "wfa-max-threads", required_argument, 0, 1007 },
/* Other alignment parameters */
{ "bandwidth", required_argument, 0, 2000 },
/* Misc */
{ "check", required_argument, 0, 'c' },
{ "check-distance", required_argument, 0, 3001 },
{ "check-bandwidth", required_argument, 0, 3002 },
{ "plot", optional_argument, 0, 3003 },
/* System */
{ "num-threads", required_argument, 0, 't' },
{ "batch-size", required_argument, 0, 4000 },
{ "progress", required_argument, 0, 'P' },
{ "verbose", required_argument, 0, 4001 },
{ "verbose1", no_argument, 0, 'v' },
{ "quiet", no_argument, 0, 'q' },
{ "help", no_argument, 0, 'h' },
{ 0, 0, 0, 0 } };
int c,option_index;
if (argc <= 1) {
usage();
exit(0);
}
while (1) {
c=getopt_long(argc,argv,"a:i:o:p:g:P:c:vqt:h",long_options,&option_index);
if (c==-1) break;
switch (c) {
/*
* Algorithm
*/
case 'a': {
/* Test bench */
if (strcmp(optarg,"test")==0) {
parameters.algorithm = alignment_test;
// Indel
} else if (strcmp(optarg,"indel-wfa")==0) {
parameters.algorithm = alignment_indel_wavefront;
// Edit
} else if (strcmp(optarg,"edit-bpm")==0) {
parameters.algorithm = alignment_edit_bpm;
} else if (strcmp(optarg,"edit-dp")==0) {
parameters.algorithm = alignment_edit_dp;
} else if (strcmp(optarg,"edit-dp-banded")==0) {
parameters.algorithm = alignment_edit_dp_banded;
} else if (strcmp(optarg,"edit-wfa")==0) {
parameters.algorithm = alignment_edit_wavefront;
// Gap-Linear
} else if (strcmp(optarg,"gap-linear-nw")==0 ||
strcmp(optarg,"gap-linear-dp")==0) {
parameters.algorithm = alignment_gap_linear_nw;
} else if (strcmp(optarg,"gap-linear-wfa")==0) {
parameters.algorithm = alignment_gap_linear_wavefront;
// Gap-Affine
} else if (strcmp(optarg,"gap-affine-swg")==0 ||
strcmp(optarg,"gap-affine-dp")==0) {
parameters.algorithm = alignment_gap_affine_swg;
} else if (strcmp(optarg,"gap-affine-swg-banded")==0 ||
strcmp(optarg,"gap-affine-dp-banded")==0) {
parameters.algorithm = alignment_gap_affine_swg_banded;
} else if (strcmp(optarg,"gap-affine-wfa")==0) {
parameters.algorithm = alignment_gap_affine_wavefront;
// Gap-Affine 2-Pieces
} else if (strcmp(optarg,"gap-affine2p-dp")==0) {
parameters.algorithm = alignment_gap_affine2p_dp;
} else if (strcmp(optarg,"gap-affine2p-wfa")==0) {
parameters.algorithm = alignment_gap_affine2p_wavefront;
} else {
fprintf(stderr,"Algorithm '%s' not recognized\n",optarg);
exit(1);
}
break;
}
/*
* Input/Output
*/
case 'i':
parameters.input_filename = optarg;
break;
case 'o':
parameters.output_filename = optarg;
break;
case 800: // --output-full
parameters.output_filename = optarg;
parameters.output_full = true;
break;
/*
* Penalties
*/
case 'p': { // --linear-penalties M,X,I
char* sentinel = strtok(optarg,",");
parameters.linear_penalties.match = atoi(sentinel);
sentinel = strtok(NULL,",");
parameters.linear_penalties.mismatch = atoi(sentinel);
sentinel = strtok(NULL,",");
parameters.linear_penalties.indel = atoi(sentinel);
break;
}
case 'g': { // --affine-penalties M,X,O,E
char* sentinel = strtok(optarg,",");
parameters.affine_penalties.match = atoi(sentinel);
sentinel = strtok(NULL,",");
parameters.affine_penalties.mismatch = atoi(sentinel);
sentinel = strtok(NULL,",");
parameters.affine_penalties.gap_opening = atoi(sentinel);
sentinel = strtok(NULL,",");
parameters.affine_penalties.gap_extension = atoi(sentinel);
break;
}
case 900: { // --affine2p-penalties M,X,O1,E1,O2,E2
char* sentinel = strtok(optarg,",");
parameters.affine2p_penalties.match = atoi(sentinel);
sentinel = strtok(NULL,",");
parameters.affine2p_penalties.mismatch = atoi(sentinel);
sentinel = strtok(NULL,",");
parameters.affine2p_penalties.gap_opening1 = atoi(sentinel);
sentinel = strtok(NULL,",");
parameters.affine2p_penalties.gap_extension1 = atoi(sentinel);
sentinel = strtok(NULL,",");
parameters.affine2p_penalties.gap_opening2 = atoi(sentinel);
sentinel = strtok(NULL,",");
parameters.affine2p_penalties.gap_extension2 = atoi(sentinel);
break;
}
case 901: { // --ends-free P0,Pf,T0,Tf
parameters.endsfree = true;
char* sentinel = strtok(optarg,",");
parameters.pattern_begin_free = atof(sentinel);
sentinel = strtok(NULL,",");
parameters.pattern_end_free = atof(sentinel);
sentinel = strtok(NULL,",");
parameters.text_begin_free = atof(sentinel);
sentinel = strtok(NULL,",");
parameters.text_end_free = atof(sentinel);
break;
}
/*
* Wavefront parameters
*/
case 1000: // --wfa-score-only
parameters.wfa_score_only = true;
break;
case 1001: // --wfa-memory-mode in {'high','med','low'}
if (strcmp(optarg,"high")==0) {
parameters.wfa_memory_mode = wavefront_memory_high;
} else if (strcmp(optarg,"med")==0) {
parameters.wfa_memory_mode = wavefront_memory_med;
} else if (strcmp(optarg,"low")==0) {
parameters.wfa_memory_mode = wavefront_memory_low;
} else if (strcmp(optarg,"ultralow")==0) {
parameters.wfa_memory_mode = wavefront_memory_ultralow;
} else {
fprintf(stderr,"Option '--wfa-memory-mode' must be in {'high','med','low','ultralow'}\n");
exit(1);
}
break;
case 1002: // --wfa-heuristic in {'none'|'banded-static'|'banded-adaptive'|'wfa-adaptive'|'xdrop'|'zdrop'}
if (strcmp(optarg,"none")==0) {
parameters.wfa_heuristic = wf_heuristic_none;
} else if (strcmp(optarg,"banded-static")==0 || strcmp(optarg,"banded")==0) {
parameters.wfa_heuristic = wf_heuristic_banded_static;
} else if (strcmp(optarg,"banded-adaptive")==0) {
parameters.wfa_heuristic = wf_heuristic_banded_adaptive;
} else if (strcmp(optarg,"wfa-adaptive")==0) {
parameters.wfa_heuristic = wf_heuristic_wfadaptive;
} else if (strcmp(optarg,"xdrop")==0) {
parameters.wfa_heuristic = wf_heuristic_xdrop;
} else if (strcmp(optarg,"zdrop")==0) {
parameters.wfa_heuristic = wf_heuristic_zdrop;
} else {
fprintf(stderr,"Option '--wf-heuristic' must be in {'none'|'banded-static'|'banded-adaptive'|'wfa-adaptive'|'xdrop'|'zdrop'}\n");
exit(1);
}
break;
case 1003: { // --wfa-heuristic-parameters <P1>,<P2>[,<P3>]
char* sentinel = strtok(optarg,",");
const int p1 = atoi(sentinel);
parameters.wfa_heuristic_p1 = p1;
sentinel = strtok(NULL,",");
const int p2 = atoi(sentinel);
parameters.wfa_heuristic_p2 = p2;
sentinel = strtok(NULL,",");
if (sentinel != NULL) {
const int p3 = atoi(sentinel);
parameters.wfa_heuristic_p3 = p3;
}
break;
}
case 1004: // --wfa-custom-match-funct
parameters.wfa_match_funct = match_function;
parameters.wfa_match_funct_arguments = &match_function_params;
break;
case 1005: // --wfa-max-memory
parameters.wfa_max_memory = atol(optarg);
break;
case 1006: // --wfa-max-score
parameters.wfa_max_score = atoi(optarg);
break;
case 1007: // --wfa-max-threads
parameters.wfa_max_threads = atoi(optarg);
break;
/*
* Other alignment parameters
*/
case 2000: // --bandwidth
parameters.bandwidth = atoi(optarg);
break;
/*
* Misc
*/
case 'c':
if (optarg == NULL) { // default = correct
parameters.check_correct = true;
parameters.check_score = false;
parameters.check_alignments = false;
} else if (strcasecmp(optarg,"display")==0) {
parameters.check_display = true;
} else if (strcasecmp(optarg,"correct")==0) {
parameters.check_correct = true;
parameters.check_score = false;
parameters.check_alignments = false;
} else if (strcasecmp(optarg,"score")==0) {
parameters.check_correct = true;
parameters.check_score = true;
parameters.check_alignments = false;
} else if (strcasecmp(optarg,"alignment")==0) {
parameters.check_correct = true;
parameters.check_score = true;
parameters.check_alignments = true;
} else {
fprintf(stderr,"Option '--check' must be in {'correct','score','alignment'}\n");
exit(1);
}
break;
case 3001: // --check-distance in {'indel','edit','linear','affine','affine2p'}
if (strcasecmp(optarg,"indel")==0) {
parameters.check_metric = ALIGN_DEBUG_CHECK_DISTANCE_METRIC_INDEL;
} else if (strcasecmp(optarg,"edit")==0) {
parameters.check_metric = ALIGN_DEBUG_CHECK_DISTANCE_METRIC_EDIT;
} else if (strcasecmp(optarg,"linear")==0) {
parameters.check_metric = ALIGN_DEBUG_CHECK_DISTANCE_METRIC_GAP_LINEAR;
} else if (strcasecmp(optarg,"affine")==0) {
parameters.check_metric = ALIGN_DEBUG_CHECK_DISTANCE_METRIC_GAP_AFFINE;
} else if (strcasecmp(optarg,"affine2p")==0) {
parameters.check_metric = ALIGN_DEBUG_CHECK_DISTANCE_METRIC_GAP_AFFINE2P;
} else {
fprintf(stderr,"Option '--check-distance' must be in {'indel','edit','linear','affine','affine2p'}\n");
exit(1);
}
break;
case 3002: // --check-bandwidth
parameters.check_bandwidth = atoi(optarg);
break;
case 3003: // --plot
parameters.plot = (optarg==NULL) ? 1 : atoi(optarg);
break;
/*
* System
*/
case 't': // --num-threads
parameters.num_threads = atoi(optarg);
break;
case 4000: // --batch-size
parameters.batch_size = atoi(optarg);
break;
case 'P':
parameters.progress = atoi(optarg);
break;
case 'v':
parameters.verbose = 1;
break;
case 4001: // --verbose (long option)
parameters.verbose = atoi(optarg);
if (parameters.verbose < 0 || parameters.verbose > 4) {
fprintf(stderr,"Option '--verbose' must be in {0,1,2,3,4}\n");
exit(1);
}
break;
case 'q':
parameters.verbose = -1;
break;
case 'h':
usage();
exit(1);
// Other
case '?': default:
fprintf(stderr,"Option not recognized \n");
exit(1);
}
}
// Checks general
if (parameters.algorithm!=alignment_test && parameters.input_filename==NULL) {
fprintf(stderr,"Option --input is required \n");
exit(1);
}
// Check 'ends-free' parameter
if (parameters.endsfree) {
switch (parameters.algorithm) {
case alignment_gap_affine_swg:
parameters.algorithm = alignment_gap_affine_swg_endsfree;
break;
case alignment_indel_wavefront:
case alignment_edit_wavefront:
case alignment_gap_linear_wavefront:
case alignment_gap_affine_wavefront:
case alignment_gap_affine2p_wavefront:
break;
default:
fprintf(stderr,"Ends-free variant not implemented for the selected algorithm\n");
exit(1);
break;
}
}
// Check 'bandwidth' parameter
switch (parameters.algorithm) {
case alignment_edit_dp_banded:
case alignment_gap_affine_swg_banded:
if (parameters.bandwidth == -1) {
fprintf(stderr,"Parameter 'bandwidth' has to be provided for banded algorithms\n");
exit(1);
}
break;
default:
if (parameters.bandwidth != -1) {
fprintf(stderr,"Parameter 'bandwidth' has no effect with the selected algorithm\n");
exit(1);
}
break;
}
// Check 'wfa-heuristic'
switch (parameters.wfa_heuristic) {
case wf_heuristic_banded_static:
case wf_heuristic_xdrop:
case wf_heuristic_zdrop:
if (parameters.wfa_heuristic_p1 == -1 ||
parameters.wfa_heuristic_p2 == -1) {
fprintf(stderr,"Heuristic requires parameters '--wfa-heuristic-parameters' <P1>,<P2>\n");
exit(1);
}
break;
case wf_heuristic_banded_adaptive:
case wf_heuristic_wfadaptive:
if (parameters.wfa_heuristic_p1 == -1 ||
parameters.wfa_heuristic_p2 == -1 ||
parameters.wfa_heuristic_p3 == -1) {
fprintf(stderr,"Heuristic requires parameters '--wfa-heuristic-parameters' <P1>,<P2>,<P3>\n");
exit(1);
}
break;
default:
break;
}
// Checks parallel
if (parameters.num_threads > 1) {
if (parameters.plot > 0) {
fprintf(stderr,"Parameter 'plot' disabled for parallel executions\n");
parameters.plot = 0;
}
}
}
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