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// =============================================================== //
// //
// File : arb_2_bin.cxx //
// Purpose : //
// //
// Institute of Microbiology (Technical University Munich) //
// http://www.arb-home.de/ //
// //
// =============================================================== //
#include <arbdbt.h>
int ARB_main(int argc, char *argv[]) {
GB_ERROR error = 0;
fprintf(stderr, "arb_2_bin - ARB database ascii to binary converter\n");
if (argc <= 1 || strcmp(argv[1], "--help") == 0) {
fprintf(stderr,
"\n"
"Purpose: Converts a database to binary format\n"
"Syntax: arb_2_bin [Options] database [newdatabase]\n"
"Options: -m create map file too\n"
" -r try to repair destroyed database\n"
" -c[tree_xxx] optimize database using tree_xxx or largest tree\n"
"\n"
"database my be '-' in which case arb_2_bin reads from stdin.\n"
"\n"
);
if (strcmp(argv[1], "--help") != 0) { error = "Missing arguments"; }
}
else {
char rtype[256];
char wtype[256];
int ci = 1;
int nidx = 0;
const char *opt_tree = 0;
{
char *rtypep = rtype;
char *wtypep = wtype;
memset(rtype, 0, 10);
memset(wtype, 0, 10);
*(wtypep++) = 'b';
*(rtypep++) = 'r';
*(rtypep++) = 'w';
while (argv[ci][0] == '-' && argv[ci][1] != 0) {
if (!strcmp(argv[ci], "-m")) { ci++; *(wtypep++) = 'm'; }
if (!strcmp(argv[ci], "-r")) { ci++; *(rtypep++) = 'R'; }
if (!strncmp(argv[ci], "-c", 2)) { opt_tree = argv[ci]+2; ci++; }
if (!strncmp(argv[ci], "-i", 2)) { nidx = atoi(argv[ci]+2); ci++; }
}
}
const char *in = argv[ci++];
const char *out = ci >= argc ? in : argv[ci++];
printf("Reading database...\n");
GB_shell shell;
GBDATA *gb_main = GBT_open(in, rtype);
if (!gb_main) {
error = GB_await_error();
}
else {
if (opt_tree) {
char *ali_name;
{
GB_transaction ta(gb_main);
ali_name = GBT_get_default_alignment(gb_main);
}
if (!strlen(opt_tree)) opt_tree = 0;
printf("Optimizing database...\n");
error = GBT_compress_sequence_tree2(gb_main, opt_tree, ali_name);
if (error) error = GBS_global_string("Error during optimize: %s", error);
free(ali_name);
}
if (!error) {
GB_set_next_main_idx(nidx);
printf("Saving database...\n");
error = GB_save(gb_main, out, wtype);
}
GB_close(gb_main);
}
}
if (error) {
fprintf(stderr, "arb_2_bin: Error: %s\n", error);
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}
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