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 = 0; |
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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 | "\n" |
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28 | "database my be '-' in which case arb_2_bin reads from stdin.\n" |
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29 | "\n" |
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30 | ); |
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31 | |
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32 | if (strcmp(argv[1], "--help") != 0) { error = "Missing arguments"; } |
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33 | } |
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34 | else { |
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35 | char rtype[256]; |
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36 | char wtype[256]; |
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37 | int ci = 1; |
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38 | int nidx = 0; |
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39 | |
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40 | const char *opt_tree = 0; |
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41 | |
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42 | { |
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43 | char *rtypep = rtype; |
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44 | char *wtypep = wtype; |
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45 | |
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46 | memset(rtype, 0, 10); |
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47 | memset(wtype, 0, 10); |
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48 | *(wtypep++) = 'b'; |
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49 | *(rtypep++) = 'r'; |
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50 | *(rtypep++) = 'w'; |
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51 | |
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52 | while (argv[ci][0] == '-' && argv[ci][1] != 0) { |
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53 | if (!strcmp(argv[ci], "-m")) { ci++; *(wtypep++) = 'm'; } |
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54 | if (!strcmp(argv[ci], "-r")) { ci++; *(rtypep++) = 'R'; } |
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55 | if (!strncmp(argv[ci], "-c", 2)) { opt_tree = argv[ci]+2; ci++; } |
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56 | if (!strncmp(argv[ci], "-i", 2)) { nidx = atoi(argv[ci]+2); ci++; } |
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57 | } |
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58 | } |
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59 | |
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60 | const char *in = argv[ci++]; |
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61 | const char *out = ci >= argc ? in : argv[ci++]; |
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62 | |
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63 | printf("Reading database...\n"); |
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64 | GB_shell shell; |
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65 | GBDATA *gb_main = GBT_open(in, rtype); |
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66 | if (!gb_main) { |
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67 | error = GB_await_error(); |
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68 | } |
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69 | else { |
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70 | if (opt_tree) { |
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71 | char *ali_name; |
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72 | { |
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73 | GB_transaction ta(gb_main); |
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74 | ali_name = GBT_get_default_alignment(gb_main); |
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75 | } |
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76 | if (!strlen(opt_tree)) opt_tree = 0; |
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77 | |
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78 | printf("Optimizing database...\n"); |
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79 | error = GBT_compress_sequence_tree2(gb_main, opt_tree, ali_name); |
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80 | if (error) error = GBS_global_string("Error during optimize: %s", error); |
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81 | free(ali_name); |
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82 | } |
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83 | |
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84 | if (!error) { |
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85 | GB_set_next_main_idx(nidx); |
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86 | printf("Saving database...\n"); |
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87 | error = GB_save(gb_main, out, wtype); |
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88 | } |
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89 | GB_close(gb_main); |
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90 | } |
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91 | } |
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92 | |
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93 | if (error) { |
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94 | fprintf(stderr, "arb_2_bin: Error: %s\n", error); |
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95 | return EXIT_FAILURE; |
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96 | } |
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97 | return EXIT_SUCCESS; |
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98 | } |
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