| 1 | // =============================================================== // |
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| 2 | // // |
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| 3 | // File : arb_2_bin.cxx // |
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| 4 | // Purpose : // |
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| 5 | // // |
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| 6 | // Institute of Microbiology (Technical University Munich) // |
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| 7 | // http://www.arb-home.de/ // |
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| 8 | // // |
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| 9 | // =============================================================== // |
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| 10 | |
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| 11 | |
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| 12 | #include <arbdbt.h> |
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| 13 | |
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| 14 | int ARB_main(int argc, char *argv[]) { |
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| 15 | GB_ERROR error = NULp; |
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| 16 | |
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| 17 | fprintf(stderr, "arb_2_bin - ARB database ascii to binary converter\n"); |
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| 18 | |
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| 19 | if (argc <= 1 || strcmp(argv[1], "--help") == 0) { |
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| 20 | fprintf(stderr, |
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| 21 | "\n" |
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| 22 | "Purpose: Converts a database to binary format\n" |
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| 23 | "Syntax: arb_2_bin [Options] database [newdatabase]\n" |
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| 24 | "Options: -m create map file too\n" |
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| 25 | " -r try to repair destroyed database\n" |
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| 26 | " -c[tree_xxx] optimize database using tree_xxx or largest tree\n" |
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| 27 | " -C<type> use extra compression\n" |
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| 28 | " (known <type>s: %s)\n" |
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| 29 | "\n" |
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| 30 | "database my be '-' in which case arb_2_bin reads from stdin.\n" |
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| 31 | "\n", |
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| 32 | GB_get_supported_compression_flags(true)); |
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| 33 | |
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| 34 | if (argc>1 && strcmp(argv[1], "--help") != 0) { error = "Missing arguments"; } |
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| 35 | } |
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| 36 | else { |
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| 37 | char rtype[256]; |
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| 38 | char wtype[256]; |
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| 39 | int ci = 1; |
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| 40 | int nidx = 0; |
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| 41 | |
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| 42 | const char *opt_tree = NULp; |
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| 43 | |
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| 44 | { |
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| 45 | char *rtypep = rtype; |
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| 46 | char *wtypep = wtype; |
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| 47 | |
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| 48 | memset(rtype, 0, 10); |
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| 49 | memset(wtype, 0, 10); |
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| 50 | *(wtypep++) = 'b'; |
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| 51 | *(rtypep++) = 'r'; |
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| 52 | *(rtypep++) = 'w'; |
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| 53 | |
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| 54 | while (argv[ci] && argv[ci][0] == '-' && argv[ci][1] != 0 && !error) { |
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| 55 | if (!strcmp(argv[ci], "-m")) { ci++; *(wtypep++) = 'm'; } |
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| 56 | else if (!strcmp(argv[ci], "-r")) { ci++; *(rtypep++) = 'R'; } |
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| 57 | else if (!strncmp(argv[ci], "-c", 2)) { opt_tree = argv[ci]+2; ci++; } |
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| 58 | else if (!strncmp(argv[ci], "-i", 2)) { nidx = atoi(argv[ci]+2); ci++; } |
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| 59 | else if (!strncmp(argv[ci], "-C", 2)) { |
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| 60 | char cflag = argv[ci][2]; ci++; |
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| 61 | if (!strchr(GB_get_supported_compression_flags(false), cflag)) { |
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| 62 | error = GBS_global_string("Unknown compression flag '%c'", cflag); |
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| 63 | } |
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| 64 | else { |
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| 65 | *(wtypep++) = cflag; |
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| 66 | } |
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| 67 | } |
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| 68 | else { |
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| 69 | error = GBS_global_string("Unknown argument '%s'", argv[ci]); |
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| 70 | break; |
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| 71 | } |
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| 72 | } |
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| 73 | } |
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| 74 | |
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| 75 | const char *in = argv[ci++]; |
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| 76 | const char *out = ci >= argc ? in : argv[ci++]; |
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| 77 | |
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| 78 | if (!error && !in) error = "missing arguments"; |
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| 79 | |
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| 80 | if (!error) { |
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| 81 | printf("Reading database...\n"); |
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| 82 | GB_shell shell; |
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| 83 | GBDATA *gb_main = GBT_open(in, rtype); |
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| 84 | if (!gb_main) { |
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| 85 | error = GB_await_error(); |
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| 86 | } |
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| 87 | else { |
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| 88 | if (opt_tree) { |
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| 89 | char *ali_name; |
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| 90 | { |
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| 91 | GB_transaction ta(gb_main); |
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| 92 | ali_name = GBT_get_default_alignment(gb_main); |
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| 93 | } |
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| 94 | if (!strlen(opt_tree)) opt_tree = NULp; |
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| 95 | |
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| 96 | printf("Optimizing database...\n"); |
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| 97 | error = GBT_compress_sequence_tree2(gb_main, opt_tree, ali_name); |
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| 98 | if (error) error = GBS_global_string("Error during optimize: %s", error); |
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| 99 | free(ali_name); |
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| 100 | } |
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| 101 | |
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| 102 | if (!error) { |
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| 103 | GB_set_next_main_idx(nidx); |
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| 104 | printf("Saving database...\n"); |
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| 105 | error = GB_save(gb_main, out, wtype); |
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| 106 | } |
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| 107 | GB_close(gb_main); |
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| 108 | } |
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| 109 | } |
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| 110 | } |
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| 111 | |
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| 112 | if (error) { |
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| 113 | fprintf(stderr, "arb_2_bin: Error: %s\n", error); |
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| 114 | return EXIT_FAILURE; |
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| 115 | } |
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| 116 | return EXIT_SUCCESS; |
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| 117 | } |
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