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#include <unistd.h>
#include <stdlib.h>
#include <string.h>
#include <stdio.h>
#include <math.h>
#include "bwt.h"
#include "bwtsw2.h"
#include "utils.h"
#include "bwa.h"
int bwa_bwtsw2(int argc, char *argv[])
bsw2opt_t *opt;
bwaidx_t *idx;
int c;
opt = bsw2_init_opt();
while ((c = getopt(argc, argv, "q:r:a:b:t:T:w:d:z:m:s:c:N:Hf:MI:SG:C")) >= 0) {
switch (c) {
case 'q': opt->q = atoi(optarg); break;
case 'r': opt->r = atoi(optarg); break;
case 'a': opt->a = atoi(optarg); break;
case 'b': opt->b = atoi(optarg); break;
case 'w': opt->bw = atoi(optarg); break;
case 'T': opt->t = atoi(optarg); break;
case 't': opt->n_threads = atoi(optarg); break;
case 'z': opt->z = atoi(optarg); break;
case 's': opt->is = atoi(optarg); break;
case 'm': opt->mask_level = atof(optarg); break;
case 'c': opt->coef = atof(optarg); break;
case 'N': opt->t_seeds = atoi(optarg); break;
case 'M': opt->multi_2nd = 1; break;
case 'H': opt->hard_clip = 1; break;
case 'f': xreopen(optarg, "w", stdout); break;
case 'I': opt->max_ins = atoi(optarg); break;
case 'S': opt->skip_sw = 1; break;
case 'C': opt->cpy_cmt = 1; break;
case 'G': opt->max_chain_gap = atoi(optarg); break;
default: return 1;
opt->qr = opt->q + opt->r;
if (optind + 2 > argc) {
fprintf(stderr, "\n");
fprintf(stderr, "Usage: bwa bwasw [options] <target.prefix> <query.fa> [query2.fa]\n\n");
fprintf(stderr, "Options: -a INT score for a match [%d]\n", opt->a);
fprintf(stderr, " -b INT mismatch penalty [%d]\n", opt->b);
fprintf(stderr, " -q INT gap open penalty [%d]\n", opt->q);
fprintf(stderr, " -r INT gap extension penalty [%d]\n", opt->r);
fprintf(stderr, " -w INT band width [%d]\n", opt->bw);
fprintf(stderr, " -m FLOAT mask level [%.2f]\n", opt->mask_level);
fprintf(stderr, "\n");
fprintf(stderr, " -t INT number of threads [%d]\n", opt->n_threads);
fprintf(stderr, " -f FILE file to output results to instead of stdout\n");
fprintf(stderr, " -H in SAM output, use hard clipping instead of soft clipping\n");
fprintf(stderr, " -C copy FASTA/Q comment to SAM output\n");
fprintf(stderr, " -M mark multi-part alignments as secondary\n");
fprintf(stderr, " -S skip Smith-Waterman read pairing\n");
fprintf(stderr, " -I INT ignore pairs with insert >=INT for inferring the size distr [%d]\n", opt->max_ins);
fprintf(stderr, "\n");
fprintf(stderr, " -T INT score threshold divided by a [%d]\n", opt->t);
fprintf(stderr, " -c FLOAT coefficient of length-threshold adjustment [%.1f]\n", opt->coef);
fprintf(stderr, " -z INT Z-best [%d]\n", opt->z);
fprintf(stderr, " -s INT maximum seeding interval size [%d]\n", opt->is);
fprintf(stderr, " -N INT # seeds to trigger rev aln; 2*INT is also the chaining threshold [%d]\n", opt->t_seeds);
fprintf(stderr, " -G INT maximum gap size during chaining [%d]\n", opt->max_chain_gap);
fprintf(stderr, "\n");
fprintf(stderr, "Note: For long Illumina, 454 and Sanger reads, assembly contigs, fosmids and\n");
fprintf(stderr, " BACs, the default setting usually works well. For the current PacBio\n");
fprintf(stderr, " reads (end of 2010), '-b5 -q2 -r1 -z10' is recommended. One may also\n");
fprintf(stderr, " increase '-z' for better sensitivity.\n");
fprintf(stderr, "\n");
return 1;
// adjust opt for opt->a
opt->t *= opt->a;
opt->coef *= opt->a;
if ((idx = bwa_idx_load(argv[optind], BWA_IDX_BWT|BWA_IDX_BNS)) == 0) return 1;
bsw2_aln(opt, idx->bns, idx->bwt, argv[optind+1], optind+2 < argc? argv[optind+2] : 0);
return 0;
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