fast-bwa/fastmap.c

#include <zlib.h>
#include <unistd.h>
#include <stdio.h>
#include "bwt.h"
#include "kvec.h"
#include "kseq.h"
KSEQ_INIT(gzFile, gzread)

extern unsigned char nst_nt4_table[256];

int main_fastmap(int argc, char *argv[])
{
	int c, i;
	kseq_t *seq;
	gzFile fp;
	bwt_t *bwt;
	bwtintv_v a[3], mem, *tvec[3];
	while ((c = getopt(argc, argv, "")) >= 0) {
		switch (c) {
		}
	}
	if (optind + 1 >= argc) {
		fprintf(stderr, "bwa fastmap <idxbase> <in.fq>\n");
		return 1;
	}
	fp = gzopen(argv[optind + 1], "r");
	seq = kseq_init(fp);
	{ // load the BWT
		char *tmp = calloc(strlen(argv[optind]) + 5, 1);
		strcat(strcpy(tmp, argv[optind]), ".bwt");
		bwt = bwt_restore_bwt(tmp);
		free(tmp);
	}
	for (i = 0; i < 3; ++i) {
		kv_init(a[i]);
		tvec[i] = &a[i];
	}
	kv_init(mem);
	while (kseq_read(seq) >= 0) {
		for (i = 0; i < seq->seq.l; ++i)
			seq->seq.s[i] = nst_nt4_table[(int)seq->seq.s[i]];
		{
			int beg = 97;
			uint8_t str[3];
			bwtint_t b, e;
			bwtintv_t ik, ok[4];
			bwt_set_intv(bwt, seq->seq.s[seq->seq.l - 1], ik);
			for (i = seq->seq.l - 2; i >= beg; --i) {
				//printf("[%lld,%lld,%lld] @ %d\n", ik.x[0], ik.x[1], ik.x[2], i+1);
				bwt_extend(bwt, &ik, ok, 1);
				ik = ok[seq->seq.s[i]];
				if (ik.x[2] == 0) break;
			}
			printf("[%lld,%lld,%lld] @ %d\n", ik.x[0], ik.x[1], ik.x[2], i+1);
			//str[0] = '\1'; str[1] = '\3'; bwt_match_exact(bwt, 2, str, &b, &e); printf("%lld,%lld,%lld\n", b, e, e-b+1);
			printf("======================== %lld, [%lld,%lld,%lld,%lld]\n", bwt->primary, bwt->L2[1], bwt->L2[2]-bwt->L2[1], bwt->L2[3]-bwt->L2[2], bwt->L2[4]-bwt->L2[3]);
			bwt_set_intv(bwt, seq->seq.s[beg], ik);
			for (i = beg + 1; i < seq->seq.l; ++i) {
				//printf("[%lld,%lld,%lld] @ %d\n", ik.x[0], ik.x[1], ik.x[2], i-1);
				bwt_extend(bwt, &ik, ok, 0);
				ik = ok[3-seq->seq.s[i]];
				if (ik.x[2] == 0) break;
			}
			printf("[%lld,%lld,%lld] @ %d\n", ik.x[0], ik.x[1], ik.x[2], i-1);
			//str[0] = '\0'; str[1] = '\2'; bwt_match_exact(bwt, 2, str, &b, &e); printf("%lld,%lld,%lld\n", b, e, e-b+1);
		}
		bwt_smem(bwt, seq->seq.l, (uint8_t*)seq->seq.s, &mem, tvec);
		printf(">%s\t%ld\n", seq->name.s, mem.n);
		for (i = 0; i < mem.n; ++i) {
			bwtintv_t *p = &mem.a[i];
			printf("%d\t%d\t%ld\n", (uint32_t)(p->info>>32), (uint32_t)p->info, (long)p->x[2]);
		}
		puts("//");
	}
	free(mem.a);
	for (i = 0; i < 3; ++i) free(a[i].a);
	bwt_destroy(bwt);
	kseq_destroy(seq);
	gzclose(fp);
	return 0;
}