text: #include <stdio.h>
  #include <unistd.h>
  #include <math.h>
  #include <stdlib.h>
  #include <string.h>
  #include <time.h>
  #include <stdint.h>
  #ifdef HAVE_CONFIG_H
  #include "config.h"
  #endif
  #include "bwtaln.h"
  #include "bwtgap.h"
  #include "utils.h"
  
  #ifdef HAVE_PTHREAD
  #define THREAD_BLOCK_SIZE 1024
  #include <pthread.h>
  static pthread_mutex_t g_seq_lock = PTHREAD_MUTEX_INITIALIZER;
  #endif
  
  gap_opt_t *gap_init_opt()
  {
  	gap_opt_t *o;
  	o = (gap_opt_t*)calloc(1, sizeof(gap_opt_t));
  	/* IMPORTANT: s_mm*10 should be about the average base error
  	   rate. Voilating this requirement will break pairing! */
  	o->s_mm = 3; o->s_gapo = 11; o->s_gape = 4;
  	o->max_diff = -1; o->max_gapo = 1; o->max_gape = 6;
  	o->indel_end_skip = 5; o->max_del_occ = 10; o->max_entries = 2000000;
  	o->mode = BWA_MODE_GAPE | BWA_MODE_COMPREAD;
  	o->seed_len = 32; o->max_seed_diff = 2;
  	o->fnr = 0.04;
  	o->n_threads = 1;
  	o->max_top2 = 30;
  	o->trim_qual = 0;
  	return o;
  }
  
  int bwa_cal_maxdiff(int l, double err, double thres)
  {
  	double elambda = exp(-l * err);
  	double sum, y = 1.0;
  	int k, x = 1;
  	for (k = 1, sum = elambda; k < 1000; ++k) {
  		y *= l * err;
  		x *= k;
  		sum += elambda * y / x;
  		if (1.0 - sum < thres) return k;
  	}
  	return 2;
  }
  
  // width must be filled as zero
  static int bwt_cal_width(const bwt_t *rbwt, int len, const ubyte_t *str, bwt_width_t *width)
  {
  	bwtint_t k, l, ok, ol;
  	int i, bid;
  	bid = 0;
  	k = 0; l = rbwt->seq_len;
  	for (i = 0; i < len; ++i) {
  		ubyte_t c = str[i];
  		if (c < 4) {
  			bwt_2occ(rbwt, k - 1, l, c, &ok, &ol);
  			k = rbwt->L2[c] + ok + 1;
  			l = rbwt->L2[c] + ol;
  		}
  		if (k > l || c > 3) { // then restart
  			k = 0;
  			l = rbwt->seq_len;
  			++bid;
  		}
  		width[i].w = l - k + 1;
  		width[i].bid = bid;
  	}
  	width[len].w = 0;
  	width[len].bid = ++bid;
  	return bid;
  }
  
  void bwa_cal_sa_reg_gap(int tid, bwt_t *const bwt[2], int n_seqs, bwa_seq_t *seqs, const gap_opt_t *opt)
  {
  	int i, max_l = 0, max_len;
  	gap_stack_t *stack;
  	bwt_width_t *w[2], *seed_w[2];
  	const ubyte_t *seq[2];
  	gap_opt_t local_opt = *opt;
  
  	// initiate priority stack
  	for (i = max_len = 0; i != n_seqs; ++i)
  		if (seqs[i].len > max_len) max_len = seqs[i].len;
  	if (opt->fnr > 0.0) local_opt.max_diff = bwa_cal_maxdiff(max_len, BWA_AVG_ERR, opt->fnr);
  	if (local_opt.max_diff < local_opt.max_gapo) local_opt.max_gapo = local_opt.max_diff;
  	stack = gap_init_stack(local_opt.max_diff, local_opt.max_gapo, local_opt.max_gape, &local_opt);
  
  	seed_w[0] = (bwt_width_t*)calloc(opt->seed_len+1, sizeof(bwt_width_t));
  	seed_w[1] = (bwt_width_t*)calloc(opt->seed_len+1, sizeof(bwt_width_t));
  	w[0] = w[1] = 0;
  	for (i = 0; i != n_seqs; ++i) {
  		bwa_seq_t *p = seqs + i;
  #ifdef HAVE_PTHREAD
  		if (opt->n_threads > 1) {
  			pthread_mutex_lock(&g_seq_lock);
  			if (p->tid < 0) { // unassigned
  				int j;
  				for (j = i; j < n_seqs && j < i + THREAD_BLOCK_SIZE; ++j)
  					seqs[j].tid = tid;
  			} else if (p->tid != tid) {
  				pthread_mutex_unlock(&g_seq_lock);
  				continue;
  			}
  			pthread_mutex_unlock(&g_seq_lock);
  		}
  #endif
  		p->sa = 0; p->type = BWA_TYPE_NO_MATCH; p->c1 = p->c2 = 0; p->n_aln = 0; p->aln = 0;
  		seq[0] = p->seq; seq[1] = p->rseq;
  		if (max_l < p->len) {
  			max_l = p->len;
  			w[0] = (bwt_width_t*)calloc(max_l + 1, sizeof(bwt_width_t));
  			w[1] = (bwt_width_t*)calloc(max_l + 1, sizeof(bwt_width_t));
  		}
  		bwt_cal_width(bwt[0], p->len, seq[0], w[0]);
  		bwt_cal_width(bwt[1], p->len, seq[1], w[1]);
  		if (opt->fnr > 0.0) local_opt.max_diff = bwa_cal_maxdiff(p->len, BWA_AVG_ERR, opt->fnr);
  		local_opt.seed_len = opt->seed_len < p->len? opt->seed_len : 0x7fffffff;
  		if (p->len > opt->seed_len) {
  			bwt_cal_width(bwt[0], opt->seed_len, seq[0] + (p->len - opt->seed_len), seed_w[0]);
  			bwt_cal_width(bwt[1], opt->seed_len, seq[1] + (p->len - opt->seed_len), seed_w[1]);
  		}
  		// core function
  		p->aln = bwt_match_gap(bwt, p->len, seq, w, p->len <= opt->seed_len? 0 : seed_w, &local_opt, &p->n_aln, stack);
  		// store the alignment
  		free(p->name); free(p->seq); free(p->rseq); free(p->qual);
  		p->name = 0; p->seq = p->rseq = p->qual = 0;
  	}
  	free(seed_w[0]); free(seed_w[1]);
  	free(w[0]); free(w[1]);
  	gap_destroy_stack(stack);
  }
  
  #ifdef HAVE_PTHREAD
  typedef struct {
  	int tid;
  	bwt_t *bwt[2];
  	int n_seqs;
  	bwa_seq_t *seqs;
  	const gap_opt_t *opt;
  } thread_aux_t;
  
  static void *worker(void *data)
  {
  	thread_aux_t *d = (thread_aux_t*)data;
  	bwa_cal_sa_reg_gap(d->tid, d->bwt, d->n_seqs, d->seqs, d->opt);
  	return 0;
  }
  #endif
  
  void bwa_aln_core(const char *prefix, const char *fn_fa, const gap_opt_t *opt)
  {
  	int i, n_seqs, tot_seqs = 0;
  	bwa_seq_t *seqs;
  	bwa_seqio_t *ks;
  	clock_t t;
  	bwt_t *bwt[2];
  
  	// initialization
  	ks = bwa_seq_open(fn_fa);
  
  	{ // load BWT
  		char *str = (char*)calloc(strlen(prefix) + 10, 1);
  		strcpy(str, prefix); strcat(str, ".bwt");  bwt[0] = bwt_restore_bwt(str);
  		strcpy(str, prefix); strcat(str, ".rbwt"); bwt[1] = bwt_restore_bwt(str);
  		free(str);
  	}
  
  	// core loop
  	fwrite(opt, sizeof(gap_opt_t), 1, stdout);
  	while ((seqs = bwa_read_seq(ks, 0x40000, &n_seqs, opt->mode & BWA_MODE_COMPREAD, opt->trim_qual)) != 0) {
  		tot_seqs += n_seqs;
  		t = clock();
  
  		fprintf(stderr, "[bwa_aln_core] calculate SA coordinate... ");
  
  #ifdef HAVE_PTHREAD
  		if (opt->n_threads <= 1) { // no multi-threading at all
  			bwa_cal_sa_reg_gap(0, bwt, n_seqs, seqs, opt);
  		} else {
  			pthread_t *tid;
  			pthread_attr_t attr;
  			thread_aux_t *data;
  			int j;
  			pthread_attr_init(&attr);
  			pthread_attr_setdetachstate(&attr, PTHREAD_CREATE_JOINABLE);
  			data = (thread_aux_t*)calloc(opt->n_threads, sizeof(thread_aux_t));
  			tid = (pthread_t*)calloc(opt->n_threads, sizeof(pthread_t));
  			for (j = 0; j < opt->n_threads; ++j) {
  				data[j].tid = j; data[j].bwt[0] = bwt[0]; data[j].bwt[1] = bwt[1];
  				data[j].n_seqs = n_seqs; data[j].seqs = seqs; data[j].opt = opt;
  				pthread_create(&tid[j], &attr, worker, data + j);
  			}
  			for (j = 0; j < opt->n_threads; ++j) pthread_join(tid[j], 0);
  			free(data); free(tid);
  		}
  #else
  		bwa_cal_sa_reg_gap(0, bwt, n_seqs, seqs, opt);
  #endif
  
  		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
  
  		t = clock();
  		fprintf(stderr, "[bwa_aln_core] write to the disk... ");
  		for (i = 0; i < n_seqs; ++i) {
  			bwa_seq_t *p = seqs + i;
  			fwrite(&p->n_aln, 4, 1, stdout);
  			if (p->n_aln) fwrite(p->aln, sizeof(bwt_aln1_t), p->n_aln, stdout);
  		}
  		fprintf(stderr, "%.2f sec\n", (float)(clock() - t) / CLOCKS_PER_SEC); t = clock();
  
  		bwa_free_read_seq(n_seqs, seqs);
  		fprintf(stderr, "[bwa_aln_core] %d sequences have been processed.\n", tot_seqs);
  	}
  
  	// destroy
  	bwt_destroy(bwt[0]); bwt_destroy(bwt[1]);
  	bwa_seq_close(ks);
  }
  
  int bwa_aln(int argc, char *argv[])
  {
  	int c, opte = -1;
  	gap_opt_t *opt;
  
  	opt = gap_init_opt();
  	while ((c = getopt(argc, argv, "n:o:e:i:d:l:k:cLR:m:t:NM:O:E:q:f:")) >= 0) {
  		switch (c) {
  		case 'n':
  			if (strstr(optarg, ".")) opt->fnr = atof(optarg), opt->max_diff = -1;
  			else opt->max_diff = atoi(optarg), opt->fnr = -1.0;
  			break;
  		case 'o': opt->max_gapo = atoi(optarg); break;
  		case 'e': opte = atoi(optarg); break;
  		case 'M': opt->s_mm = atoi(optarg); break;
  		case 'O': opt->s_gapo = atoi(optarg); break;
  		case 'E': opt->s_gape = atoi(optarg); break;
  		case 'd': opt->max_del_occ = atoi(optarg); break;
  		case 'i': opt->indel_end_skip = atoi(optarg); break;
  		case 'l': opt->seed_len = atoi(optarg); break;
  		case 'k': opt->max_seed_diff = atoi(optarg); break;
  		case 'm': opt->max_entries = atoi(optarg); break;
  		case 't': opt->n_threads = atoi(optarg); break;
  		case 'L': opt->mode |= BWA_MODE_LOGGAP; break;
  		case 'R': opt->max_top2 = atoi(optarg); break;
  		case 'q': opt->trim_qual = atoi(optarg); break;
  		case 'c': opt->mode &= ~BWA_MODE_COMPREAD; break;
  		case 'N': opt->mode |= BWA_MODE_NONSTOP; opt->max_top2 = 0x7fffffff; break;
          case 'f': freopen(optarg, "wb", stdout); break;
  		default: return 1;
  		}
  	}
  	if (opte > 0) {
  		opt->max_gape = opte;
  		opt->mode &= ~BWA_MODE_GAPE;
  	}
  
  	if (optind + 2 > argc) {
  		fprintf(stderr, "\n");
  		fprintf(stderr, "Usage:   bwa aln [options] <prefix> <in.fq>\n\n");
  		fprintf(stderr, "Options: -n NUM    max #diff (int) or missing prob under %.2f err rate (float) [%.2f]\n",
  				BWA_AVG_ERR, opt->fnr);
  		fprintf(stderr, "         -o INT    maximum number or fraction of gap opens [%d]\n", opt->max_gapo);
  		fprintf(stderr, "         -e INT    maximum number of gap extensions, -1 for disabling long gaps [-1]\n");
  		fprintf(stderr, "         -i INT    do not put an indel within INT bp towards the ends [%d]\n", opt->indel_end_skip);
  		fprintf(stderr, "         -d INT    maximum occurrences for extending a long deletion [%d]\n", opt->max_del_occ);
  		fprintf(stderr, "         -l INT    seed length [%d]\n", opt->seed_len);
  		fprintf(stderr, "         -k INT    maximum differences in the seed [%d]\n", opt->max_seed_diff);
  		fprintf(stderr, "         -m INT    maximum entries in the queue [%d]\n", opt->max_entries);
  		fprintf(stderr, "         -t INT    number of threads [%d]\n", opt->n_threads);
  		fprintf(stderr, "         -M INT    mismatch penalty [%d]\n", opt->s_mm);
  		fprintf(stderr, "         -O INT    gap open penalty [%d]\n", opt->s_gapo);
  		fprintf(stderr, "         -E INT    gap extension penalty [%d]\n", opt->s_gape);
  		fprintf(stderr, "         -R INT    stop searching when there are >INT equally best hits [%d]\n", opt->max_top2);
  		fprintf(stderr, "         -q INT    quality threshold for read trimming down to %dbp [%d]\n", BWA_MIN_RDLEN, opt->trim_qual);
  		fprintf(stderr, "         -c        input sequences are in the color space\n");
  		fprintf(stderr, "         -L        log-scaled gap penalty for long deletions\n");
  		fprintf(stderr, "         -N        non-iterative mode: search for all n-difference hits (slooow)\n");
          fprintf(stderr, "         -f FILE   file to write output to instead of stdout\n");
  		fprintf(stderr, "\n");
  		return 1;
  	}
  	if (opt->fnr > 0.0) {
  		int i, k;
  		for (i = 17, k = 0; i <= 250; ++i) {
  			int l = bwa_cal_maxdiff(i, BWA_AVG_ERR, opt->fnr);
  			if (l != k) fprintf(stderr, "[bwa_aln] %dbp reads: max_diff = %d\n", i, l);
  			k = l;
  		}
  	}
  	bwa_aln_core(argv[optind], argv[optind+1], opt);
  	free(opt);
  	return 0;
  }
  
  /* rgoya: Temporary clone of aln_path2cigar to accomodate for bwa_cigar_t,
  __cigar_op and __cigar_len while keeping stdaln stand alone */
  bwa_cigar_t *bwa_aln_path2cigar(const path_t *path, int path_len, int *n_cigar)
  {
  	uint32_t *cigar32;
  	bwa_cigar_t *cigar;
  	int i;
  	cigar32 = aln_path2cigar32((path_t*) path, path_len, n_cigar);
  	cigar = (bwa_cigar_t*)cigar32;
  	for (i = 0; i < *n_cigar; ++i)
                  cigar[i] = __cigar_create( (cigar32[i]&0xf), (cigar32[i]>>4) );
  	return cigar;
  }
  
  