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1 #include <stdio.h>
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2 #include <string.h>
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3 #include "main.h"
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4 #include "utils.h"
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5
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6 #ifndef PACKAGE_VERSION
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7 #define PACKAGE_VERSION "0.6.2-r126"
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8 #endif
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9
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10 static int usage()
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11 {
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12 fprintf(stderr, "\n");
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13 fprintf(stderr, "Program: bwa (alignment via Burrows-Wheeler transformation)\n");
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14 fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
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15 fprintf(stderr, "Contact: Heng Li <lh3@sanger.ac.uk>\n\n");
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16 fprintf(stderr, "Usage: bwa <command> [options]\n\n");
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17 fprintf(stderr, "Command: index index sequences in the FASTA format\n");
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18 fprintf(stderr, " aln gapped/ungapped alignment\n");
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19 fprintf(stderr, " samse generate alignment (single ended)\n");
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20 fprintf(stderr, " sampe generate alignment (paired ended)\n");
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21 fprintf(stderr, " bwasw BWA-SW for long queries\n");
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22 fprintf(stderr, " fastmap identify super-maximal exact matches\n");
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23 fprintf(stderr, "\n");
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24 fprintf(stderr, " fa2pac convert FASTA to PAC format\n");
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25 fprintf(stderr, " pac2bwt generate BWT from PAC\n");
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26 fprintf(stderr, " pac2bwtgen alternative algorithm for generating BWT\n");
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27 fprintf(stderr, " bwtupdate update .bwt to the new format\n");
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28 fprintf(stderr, " bwt2sa generate SA from BWT and Occ\n");
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29 fprintf(stderr, " pac2cspac convert PAC to color-space PAC\n");
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30 fprintf(stderr, " stdsw standard SW/NW alignment\n");
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31 fprintf(stderr, "\n");
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32 return 1;
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33 }
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34
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35 void bwa_print_sam_PG()
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36 {
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37 printf("@PG\tID:bwa\tPN:bwa\tVN:%s\n", PACKAGE_VERSION);
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38 }
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39
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40 int main(int argc, char *argv[])
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41 {
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42 int i, ret;
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43 double t_real;
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44 t_real = realtime();
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45 if (argc < 2) return usage();
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46 if (strcmp(argv[1], "fa2pac") == 0) ret = bwa_fa2pac(argc-1, argv+1);
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47 else if (strcmp(argv[1], "pac2bwt") == 0) ret = bwa_pac2bwt(argc-1, argv+1);
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48 else if (strcmp(argv[1], "pac2bwtgen") == 0) ret = bwt_bwtgen_main(argc-1, argv+1);
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49 else if (strcmp(argv[1], "bwtupdate") == 0) ret = bwa_bwtupdate(argc-1, argv+1);
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50 else if (strcmp(argv[1], "bwt2sa") == 0) ret = bwa_bwt2sa(argc-1, argv+1);
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51 else if (strcmp(argv[1], "index") == 0) ret = bwa_index(argc-1, argv+1);
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52 else if (strcmp(argv[1], "aln") == 0) ret = bwa_aln(argc-1, argv+1);
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53 else if (strcmp(argv[1], "sw") == 0) ret = bwa_stdsw(argc-1, argv+1);
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54 else if (strcmp(argv[1], "samse") == 0) ret = bwa_sai2sam_se(argc-1, argv+1);
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55 else if (strcmp(argv[1], "sampe") == 0) ret = bwa_sai2sam_pe(argc-1, argv+1);
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56 else if (strcmp(argv[1], "pac2cspac") == 0) ret = bwa_pac2cspac(argc-1, argv+1);
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57 else if (strcmp(argv[1], "stdsw") == 0) ret = bwa_stdsw(argc-1, argv+1);
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58 else if (strcmp(argv[1], "bwtsw2") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
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59 else if (strcmp(argv[1], "dbwtsw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
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60 else if (strcmp(argv[1], "bwasw") == 0) ret = bwa_bwtsw2(argc-1, argv+1);
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61 else if (strcmp(argv[1], "fastmap") == 0) ret = main_fastmap(argc-1, argv+1);
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62 else {
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63 fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
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64 return 1;
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65 }
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66 err_fflush(stdout);
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67 err_fclose(stdout);
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68 if (ret == 0) {
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69 fprintf(stderr, "[%s] Version: %s\n", __func__, PACKAGE_VERSION);
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70 fprintf(stderr, "[%s] CMD:", __func__);
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71 for (i = 0; i < argc; ++i)
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72 fprintf(stderr, " %s", argv[i]);
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73 fprintf(stderr, "\n[%s] Real time: %.3f sec; CPU: %.3f sec\n", __func__, realtime() - t_real, cputime());
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74 }
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75 return 0;
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76 }
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