/*
 *  blastzWrapper.c version 10
 *
 *  -- wrapping of blastz
 */

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include "util.h"
#include "multi_util.h"
#include "seq.h"

static const char rcsid[] = "$Id: blastzWrapper.c 142 2008-11-12 18:55:23Z rico $";

#define BZ "blastz"
#define VERSION 10

// replace the first argument with the new first_fn
static char* modify_cmdline(int argc, char** argv, char* first_fn, char* second_fn, char* newcmd) {
    int i;
    sprintf(newcmd, "%s %s %s", BZ, first_fn, second_fn);
    for (i=3; i<argc; i++) {
        strcat(newcmd, " ");
        strcat(newcmd, argv[i]);
    }
    return newcmd;
}

// switch the first and second sequence
void replace_reverse_bz(FILE* fpr, FILE* fpw, char* replace_str, int contig, int rev) {
    char buf[1000], buf1[1000], buf2[1000], cmd[200], spe1[200], spe2[200];
    int b1, b2, e1, e2, pct, beg, end, dir;

    while ( fgets(buf, 1000, fpr) != NULL) {
        if ( rev==1 && strncmp(buf, "d {", 3) == 0) {
            fprintf(fpw, "%s", buf);
            fgets(buf, 1000, fpr);
            sscanf(buf, "  \"%s %s %s", cmd, spe1, spe2);
            fprintf(fpw, "  \"%s %s %s\n", cmd, spe2, spe1);
        } else if ( rev==1 && strncmp(buf, "h {",3)==0) {
            fprintf(fpw, "%s", buf);
            fgets(buf1, 1000, fpr);
            fgets(buf2, 1000, fpr);
            fprintf(fpw, buf2);
            fprintf(fpw, buf1);
        } else if ( strncmp(buf, "s {", 3) == 0) {
            fprintf(fpw, "%s", buf);
            fgets(buf1, 1000, fpr);
            sscanf(buf1, "%*s %d %d %d %*d", &beg, &end, &dir);
            sprintf(buf1, "  \"%s\" %d %d %d %d\n", replace_str, beg, end, dir, contig);
            fgets(buf2, 1000, fpr);
            if (rev==1) {
                fprintf(fpw, buf2);
                fprintf(fpw, buf1);
            } else {
                fprintf(fpw, buf1);
                fprintf(fpw, buf2);
            }
        } else if ( rev==1 && strncmp(buf, "a {", 3)==0) {
            fprintf(fpw, "%s", buf);
            fgets(buf, 1000, fpr);
            fprintf(fpw, "%s", buf);  // s
            fgets(buf, 1000, fpr);    // b
            sscanf(buf, "  b %d %d", &b1, &b2);
            fprintf(fpw, "  b %d %d\n", b2, b1);
            fgets(buf, 1000, fpr);    // e
            sscanf(buf, "  e %d %d", &e1, &e2);
            fprintf(fpw, "  e %d %d\n", e2, e1);
            fgets(buf, 1000, fpr);
            while ( strncmp(buf, "  l", 3)==0) {
                sscanf(buf, "  l %d %d %d %d %d", &b1, &b2, &e1, &e2, &pct);
                fprintf(fpw, "  l %d %d %d %d %d\n", b2, b1, e2, e1, pct);
                fgets(buf, 1000, fpr);
            }
            fprintf(fpw, "%s", buf);
        } else if ( strncmp(buf, "#:eof", 5) != 0)
            fprintf(fpw, "%s", buf);
    }
}

int main(int argc, char** argv) {
    char cmdline[500], seq_file1[500], seq_file2[500];
    int c1, c2, reverse=0, tmp, fd, contig=1;
    SEQ* sf;
    FILE* pf, *fpw;

    sprintf(cmdline, "blastzWrapper.v%d", VERSION);
    argv0 = cmdline;

    if ( argc < 3 )
        fatal(" -- wrapper of blastz, passing all arguments to blastz.\nargs: seqfile1 seqfile2 [options]");

    sf = seq_open(argv[1]);
    for (c1=0; seq_read(sf)!=0; c1++)
        ;
    seq_close(sf);
    sf = seq_open(argv[2]);
    for (c2=0; seq_read(sf)!=0; c2++)
        ;
    seq_close(sf);

    if ( c1 > c2) {
        reverse = 1;
        strcpy(seq_file1, argv[2]);
        strcpy(seq_file2, argv[1]);
        tmp = c1;
        c1 = c2;
        c2 = tmp;
    } else {
        strcpy(seq_file1, argv[1]);
        strcpy(seq_file2, argv[2]);
    }

    if (c1 == 1) {
        modify_cmdline(argc, argv, seq_file1, seq_file2, cmdline);
        if (reverse == 0) {
            system(cmdline);
            return 0;
        }
        pf = popen(cmdline, "r");
        replace_reverse_bz(pf, stdout, seq_file1, contig, 1);
        pclose(pf);
    } else {
        sf = seq_open(seq_file1);
        while ( seq_read(sf)) {
            fpw = tmpfile();
            fprintf(fpw, "%s\n", sf->header);
            fprintf(fpw, "%s\n", sf->seq);
            fseek(fpw, 0, SEEK_SET);
            fd = fileno(fpw);
            dup2(fd, 0);
            modify_cmdline(argc, argv, "/dev/stdin", seq_file2, cmdline);
            strcat(cmdline, " | grep -v eof");
            pf = popen(cmdline, "r");
            if ( reverse == 1)
                replace_reverse_bz(pf, stdout, seq_file1, contig, 1);
            else
                replace_reverse_bz(pf, stdout, seq_file1, contig, 0);
            pclose(pf);
            fclose(fpw);
            contig++;
        }
        seq_close(sf);
    }

    fprintf(stdout, "#:eof\n");
    return 0;
}