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#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <getopt.h>
#include "abpoa.h"
#include "abpoa_graph.h"
#include "abpoa_align.h"
#include "abpoa_seq.h"
#include "utils.h"
char NAME[20] = "abPOA";
char PROG[20] = "abpoa";
#define _ba BOLD UNDERLINE "a" NONE
#define _bb BOLD UNDERLINE "b" NONE
#define _bP BOLD UNDERLINE "P" NONE
#define _bO BOLD UNDERLINE "O" NONE
#define _bA BOLD UNDERLINE "A" NONE
char DESCRIPTION[100] = _ba "daptive " _bb "anded " _bP "artial " _bO "rder " _bA "lignment";
char VERSION[20] = "1.5.1";
char CONTACT[30] = "gaoy1@chop.edu";
const struct option abpoa_long_opt [] = {
{ "align-mode", 1, NULL, 'm' },
{ "match", 1, NULL, 'M' },
{ "mismatch", 1, NULL, 'X' },
{ "matrix", 1, NULL, 't' },
{ "gap-open", 1, NULL, 'O' },
{ "gap-ext", 1, NULL, 'E' },
{ "extra-b", 1, NULL, 'b' },
{ "extra-f", 1, NULL, 'f' },
{ "zdrop", 1, NULL, 'z' },
{ "bonus", 1, NULL, 'e' },
{ "seeding", 0, NULL, 'S'},
{ "k-mer", 1, NULL, 'k' },
{ "window", 1, NULL, 'w' },
{ "min-poa-win", 1, NULL, 'n' },
{ "progressive", 0, NULL, 'p'},
{ "use-qual-weight", 0, NULL, 'Q'},
{ "amino-acid", 0, NULL, 'c'},
{ "in-list", 0, NULL, 'l' },
{ "increment", 1, NULL, 'i' },
{ "amb-strand", 0, NULL, 's' },
{ "output", 1, NULL, 'o' },
{ "result", 1, NULL, 'r' },
{ "out-pog", 1, NULL, 'g' },
{ "max-num-cons", 1, NULL, 'd', },
{ "min-freq", 1, NULL, 'q', },
{ "help", 0, NULL, 'h' },
{ "version", 0, NULL, 'v' },
{ 0, 0, 0, 0}
};
int abpoa_usage(void)
{
err_printf("\n");
err_printf("%s: %s \n\n", PROG, DESCRIPTION);
err_printf("Version: %s\t", VERSION);
err_printf("Contact: %s\n\n", CONTACT);
err_printf("Usage: %s [options] <in.fa/fq> > cons.fa/msa.out/abpoa.gfa\n\n", PROG);
err_printf("Options:\n");
err_printf(" Alignment:\n");
err_printf(" -m --aln-mode INT alignment mode [%d]\n", ABPOA_GLOBAL_MODE);
err_printf(" %d: global, %d: local, %d: extension\n", ABPOA_GLOBAL_MODE, ABPOA_LOCAL_MODE, ABPOA_EXTEND_MODE);
err_printf(" -M --match INT match score [%d]\n", ABPOA_MATCH);
err_printf(" -X --mismatch INT mismatch penalty [%d]\n", ABPOA_MISMATCH);
err_printf(" -t --matrix FILE scoring matrix file, \'-M\' and \'-X\' are not used when \'-t\' is used [Null]\n");
err_printf(" e.g., \'HOXD70.mtx, BLOSUM62.mtx\'\n");
err_printf(" -O --gap-open INT(,INT) gap opening penalty (O1,O2) [%d,%d]\n", ABPOA_GAP_OPEN1, ABPOA_GAP_OPEN2);
err_printf(" -E --gap-ext INT(,INT) gap extension penalty (E1,E2) [%d,%d]\n", ABPOA_GAP_EXT1, ABPOA_GAP_EXT2);
err_printf(" %s provides three gap penalty modes, cost of a g-long gap:\n", NAME);
err_printf(" - convex (default): min{O1+g*E1, O2+g*E2}\n");
err_printf(" - affine (set O2 as 0): O1+g*E1\n");
err_printf(" - linear (set O1 as 0): g*E1\n");
err_printf(" -s --amb-strand ambiguous strand mode [False]\n");
err_printf(" for each input sequence, try the reverse complement if the current\n");
err_printf(" alignment score is too low, and pick the strand with a higher score\n");
err_printf(" Adaptive banded DP:\n");
err_printf(" -b --extra-b INT first adaptive banding parameter [%d]\n", ABPOA_EXTRA_B);
err_printf(" set b as < 0 to disable adaptive banded DP\n");
err_printf(" -f --extra-f FLOAT second adaptive banding parameter [%.2f]\n", ABPOA_EXTRA_F);
err_printf(" the number of extra bases added on both sites of the band is\n");
err_printf(" b+f*L, where L is the length of the aligned sequence\n");
// err_printf(" -z --zdrop INT Z-drop score in extension alignment [-1]\n");
// err_printf(" set as <= 0 to disable Z-drop extension\n");
// err_printf(" -e --bonus INT end bonus score in extension alignment [-1]\n");
// err_printf(" set as <= 0 to disable end bounus\n");
err_printf(" Minimizer-based seeding and partition (only effective in global alignment mode):\n");
err_printf(" -S --seeding enable minimizer-based seeding and anchoring [False]\n");
err_printf(" -k --k-mer INT minimizer k-mer size [%d]\n", ABPOA_MMK);
err_printf(" -w --window INT minimizer window size [%d]\n", ABPOA_MMW);
err_printf(" -n --min-poa-win INT min. size of window to perform POA [%d]\n", ABPOA_MIN_POA_WIN);
err_printf(" -p --progressive build guide tree and perform progressive partial order alignment [False]\n");
// err_printf(" -n --par-size minimal partition size [%d]\n", ABPOA_W);
err_printf(" Input/Output:\n");
err_printf(" -Q --use-qual-weight take base quality score from FASTQ input file as graph edge weight [False]\n");
err_printf(" -c --amino-acid input sequences are amino acid (default is nucleotide) [False]\n");
err_printf(" -l --in-list input file is a list of sequence file names [False]\n");
err_printf(" each line is one sequence file containing a set of sequences\n");
err_printf(" which will be aligned by abPOA to generate a consensus sequence\n");
err_printf(" -i --incrmnt FILE incrementally align sequences to an existing graph/MSA [Null]\n");
err_printf(" graph could be in GFA or MSA format generated by abPOA\n");
err_printf(" -o --output FILE output to FILE [stdout]\n");
err_printf(" -r --result INT output result mode [%d]\n", ABPOA_OUT_CONS);
err_printf(" - %d: consensus in FASTA format\n", ABPOA_OUT_CONS);
err_printf(" - %d: MSA in PIR format\n", ABPOA_OUT_MSA);
err_printf(" - %d: both 0 & 1\n", ABPOA_OUT_CONS_MSA);
err_printf(" - %d: graph in GFA format\n", ABPOA_OUT_GFA);
err_printf(" - %d: graph with consensus path in GFA format\n", ABPOA_OUT_CONS_GFA);
err_printf(" - %d: consensus in FASTQ format\n", ABPOA_OUT_CONS_FQ);
err_printf(" -d --maxnum-cons INT max. number of consensus sequence to generate [1]\n");
err_printf(" -q --min-freq FLOAT min. frequency of each consensus sequence (only effective when -d/--num-cons > 1) [%.2f]\n", MULTIP_MIN_FREQ);
err_printf(" -g --out-pog FILE dump final alignment graph to FILE (.pdf/.png) [Null]\n\n");
err_printf(" -h --help print this help usage information\n");
err_printf(" -v --version show version number\n");
err_printf("\n");
return 1;
}
int abpoa_main(char *file_fn, int is_list, abpoa_para_t *abpt){
double realtime0 = realtime();
// TODO abpoa_init for each input file ???
abpoa_t *ab = abpoa_init();
if (is_list) { // input file list
FILE *list_fp = fopen(file_fn, "r"); char read_fn[1024];
while (fgets(read_fn, sizeof(read_fn), list_fp)) {
read_fn[strlen(read_fn)-1] = '\0';
abpoa_msa1(ab, abpt, read_fn, stdout);
}
fclose(list_fp);
} else // input file
abpoa_msa1(ab, abpt, file_fn, stdout);
abpoa_free(ab);
err_func_printf(__func__, "Real time: %.3f sec; CPU: %.3f sec; Peak RSS: %.3f GB.", realtime() - realtime0, cputime(), peakrss() / 1024.0 / 1024.0 / 1024.0);
return 0;
}
int main(int argc, char **argv) {
int c, m, in_list=0; char *s; abpoa_para_t *abpt = abpoa_init_para();
while ((c = getopt_long(argc, argv, "m:M:X:t:O:E:b:f:z:e:QSk:w:n:i:clpso:r:g:d:q:hvV:", abpoa_long_opt, NULL)) >= 0) {
switch(c)
{
case 'm': m = atoi(optarg);
if (m != ABPOA_GLOBAL_MODE && m != ABPOA_EXTEND_MODE && m != ABPOA_LOCAL_MODE) {
err_printf("Unknown alignment mode: %d.\n", m); return abpoa_usage();
} abpt->align_mode=m; break;
case 'M': abpt->match = atoi(optarg); break;
case 'X': abpt->mismatch = atoi(optarg); break;
case 't': abpt->use_score_matrix = 1; abpt->mat_fn = strdup(optarg); break;
case 'O': abpt->gap_open1 = strtol(optarg, &s, 10); if (*s == ',') abpt->gap_open2 = strtol(s+1, &s, 10); break;
case 'E': abpt->gap_ext1 = strtol(optarg, &s, 10); if (*s == ',') abpt->gap_ext2 = strtol(s+1, &s, 10); break;
case 'b': abpt->wb = atoi(optarg); break;
case 'f': abpt->wf = atof(optarg); break;
case 'z': abpt->zdrop = atoi(optarg); break;
case 'e': abpt->end_bonus= atoi(optarg); break;
case 'Q': abpt->use_qv = 1; break;
case 'S': abpt->disable_seeding = 0; break;
case 'k': abpt->k = atoi(optarg); break;
case 'w': abpt->w = atoi(optarg); break;
case 'n': abpt->min_w = atoi(optarg); break;
case 'c': abpt->m = 27; abpt->mat = (int*)_err_realloc(abpt->mat, abpt->m * abpt->m * sizeof(int)); break;
case 'i': abpt->incr_fn = strdup(optarg); break;
case 'l': in_list = 1; break;
case 'p': abpt->progressive_poa = 1; break;
case 's': abpt->amb_strand = 1; break;
case 'o': if (strcmp(optarg, "-") != 0) {
if (freopen(optarg, "wb", stdout) == NULL)
err_fatal(__func__, "Failed to open the output file %s", optarg);
} break;
case 'r': if (atoi(optarg) == ABPOA_OUT_CONS) abpt->out_cons = 1, abpt->out_msa = 0;
else if (atoi(optarg) == ABPOA_OUT_MSA) abpt->out_cons = 0, abpt->out_msa = 1;
else if (atoi(optarg) == ABPOA_OUT_CONS_MSA) abpt->out_cons = abpt->out_msa = 1;
else if (atoi(optarg) == ABPOA_OUT_GFA) abpt->out_cons = 0, abpt->out_gfa = 1;
else if (atoi(optarg) == ABPOA_OUT_CONS_GFA) abpt->out_cons = 1, abpt->out_gfa = 1;
else if (atoi(optarg) == ABPOA_OUT_CONS_FQ) abpt->out_cons = 1, abpt->out_fq = 1;
else err_printf("Error: unknown output result mode: %s.\n", optarg);
break;
case 'g': abpt->out_pog= strdup(optarg); break;
case 'd': abpt->max_n_cons = atoi(optarg); break;
case 'q': abpt->min_freq = atof(optarg); break;
case 'h': return abpoa_usage();
case 'V': abpt->verbose = atoi(optarg); break;
case 'v': printf("%s\n", VERSION); goto End; break;
default:
err_printf("Error: unknown option: %s.\n", optarg);
return abpoa_usage();
break;
}
}
if (argc - optind != 1) return abpoa_usage();
abpoa_post_set_para(abpt);
fprintf(stderr, "[%s] CMD: ", __func__);
for (c = 0; c < argc; ++c)
fprintf(stderr, " %s", argv[c]);
fprintf(stderr, "\n");
abpoa_main(argv[optind], in_list, abpt);
End:
abpoa_free_para(abpt);
return 0;
}
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