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#include <stdlib.h>
#include <stdio.h>
#include <unistd.h>
#include <string.h>
#include <zlib.h>
#include <stdint.h>
#include "stdaln.h"
#include "utils.h"
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)
typedef struct {
int l;
unsigned char *s;
char *n;
} seq1_t;
typedef struct {
int n_seqs, m_seqs;
seq1_t *seqs;
} seqs_t;
unsigned char aln_rev_table[256] = {
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','T','V','G', 'H','N','N','C', 'D','N','N','M', 'N','K','N','N',
'N','N','Y','S', 'A','N','B','W', 'X','R','N','N', 'N','N','N','N',
'N','t','v','g', 'h','N','N','c', 'd','N','N','m', 'N','k','N','N',
'N','N','y','s', 'a','N','b','w', 'x','r','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N',
'N','N','N','N', 'N','N','N','N', 'N','N','N','N', 'N','N','N','N'
};
static int g_is_global = 0, g_thres = 1, g_strand = 0, g_aa = 0;
static AlnParam g_aln_param;
static void revseq(int len, uint8_t *seq)
{
int i;
for (i = 0; i < len>>1; ++i) {
uint8_t tmp = aln_rev_table[seq[len-1-i]];
seq[len-1-i] = aln_rev_table[seq[i]];
seq[i] = tmp;
}
if (len&1) seq[i] = aln_rev_table[seq[i]];
}
static seqs_t *load_seqs(const char *fn)
{
seqs_t *s;
seq1_t *p;
gzFile fp;
int l;
kseq_t *seq;
fp = xzopen(fn, "r");
seq = kseq_init(fp);
s = (seqs_t*)calloc(1, sizeof(seqs_t));
s->m_seqs = 256;
s->seqs = (seq1_t*)calloc(s->m_seqs, sizeof(seq1_t));
while ((l = kseq_read(seq)) >= 0) {
if (s->n_seqs == s->m_seqs) {
s->m_seqs <<= 1;
s->seqs = (seq1_t*)realloc(s->seqs, s->m_seqs * sizeof(seq1_t));
}
p = s->seqs + (s->n_seqs++);
p->l = seq->seq.l;
p->s = (unsigned char*)malloc(p->l + 1);
memcpy(p->s, seq->seq.s, p->l);
p->s[p->l] = 0;
p->n = strdup((const char*)seq->name.s);
}
kseq_destroy(seq);
gzclose(fp);
fprintf(stderr, "[load_seqs] %d sequences are loaded.\n", s->n_seqs);
return s;
}
static void aln_1seq(const seqs_t *ss, const char *name, int l, const char *s, char strand)
{
int i;
for (i = 0; i < ss->n_seqs; ++i) {
AlnAln *aa;
seq1_t *p = ss->seqs + i;
g_aln_param.band_width = l + p->l;
aa = aln_stdaln_aux(s, (const char*)p->s, &g_aln_param, g_is_global, g_thres, l, p->l);
if (aa->score >= g_thres || g_is_global) {
printf(">%s\t%d\t%d\t%s\t%c\t%d\t%d\t%d\t%d\t", p->n, aa->start1? aa->start1 : 1, aa->end1, name, strand,
aa->start2? aa->start2 : 1, aa->end2, aa->score, aa->subo);
// NB: I put the short sequence as the first sequence in SW, an insertion to
// the reference becomes a deletion from the short sequence. Therefore, I use
// "MDI" here rather than "MID", and print ->out2 first rather than ->out1.
for (i = 0; i != aa->n_cigar; ++i)
printf("%d%c", aa->cigar32[i]>>4, "MDI"[aa->cigar32[i]&0xf]);
printf("\n%s\n%s\n%s\n", aa->out2, aa->outm, aa->out1);
}
aln_free_AlnAln(aa);
}
}
static void aln_seqs(const seqs_t *ss, const char *fn)
{
gzFile fp;
kseq_t *seq;
int l;
fp = xzopen(fn, "r");
seq = kseq_init(fp);
while ((l = kseq_read(seq)) >= 0) {
if (g_strand&1) aln_1seq(ss, (char*)seq->name.s, l, seq->seq.s, '+');
if (g_strand&2) {
revseq(l, (uint8_t*)seq->seq.s);
aln_1seq(ss, (char*)seq->name.s, l, seq->seq.s, '-');
}
}
kseq_destroy(seq);
gzclose(fp);
}
int bwa_stdsw(int argc, char *argv[])
{
int c;
seqs_t *ss;
while ((c = getopt(argc, argv, "gT:frp")) >= 0) {
switch (c) {
case 'g': g_is_global = 1; break;
case 'T': g_thres = atoi(optarg); break;
case 'f': g_strand |= 1; break;
case 'r': g_strand |= 2; break;
case 'p': g_aa = 1; break;
}
}
if (g_strand == 0) g_strand = 3;
if (g_aa) g_strand = 1;
if (optind + 1 >= argc) {
fprintf(stderr, "\nUsage: bwa stdsw [options] <seq1.long.fa> <seq2.short.fa>\n\n");
fprintf(stderr, "Options: -T INT minimum score [%d]\n", g_thres);
fprintf(stderr, " -p protein alignment (suppressing -r)\n");
fprintf(stderr, " -f forward strand only\n");
fprintf(stderr, " -r reverse strand only\n");
fprintf(stderr, " -g global alignment\n\n");
fprintf(stderr, "Note: This program is specifically designed for alignment between multiple short\n");
fprintf(stderr, " sequences and ONE long sequence. It outputs the suboptimal score on the long\n");
fprintf(stderr, " sequence.\n\n");
return 1;
}
g_aln_param = g_aa? aln_param_aa2aa : aln_param_blast;
g_aln_param.gap_end = 0;
ss = load_seqs(argv[optind]);
aln_seqs(ss, argv[optind+1]);
return 0;
}