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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
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5 #ifndef PACKAGE_VERSION
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6 #define PACKAGE_VERSION "0.5.7 (r1310)"
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7 #endif
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8
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9 static int usage()
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10 {
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11 fprintf(stderr, "\n");
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12 fprintf(stderr, "Program: bwa (alignment via Burrows-Wheeler transformation)\n");
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13 fprintf(stderr, "Version: %s\n", PACKAGE_VERSION);
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14 fprintf(stderr, "Contact: Heng Li <lh3@sanger.ac.uk>\n\n");
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15 fprintf(stderr, "Usage: bwa <command> [options]\n\n");
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16 fprintf(stderr, "Command: index index sequences in the FASTA format\n");
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17 fprintf(stderr, " aln gapped/ungapped alignment\n");
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18 fprintf(stderr, " samse generate alignment (single ended)\n");
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19 fprintf(stderr, " sampe generate alignment (paired ended)\n");
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20 fprintf(stderr, " bwasw BWA-SW for long queries\n");
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21 fprintf(stderr, "\n");
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22 fprintf(stderr, " fa2pac convert FASTA to PAC format\n");
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23 fprintf(stderr, " pac2bwt generate BWT from PAC\n");
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24 fprintf(stderr, " pac2bwtgen alternative algorithm for generating BWT\n");
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25 fprintf(stderr, " bwtupdate update .bwt to the new format\n");
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26 fprintf(stderr, " pac_rev generate reverse PAC\n");
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27 fprintf(stderr, " bwt2sa generate SA from BWT and Occ\n");
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28 fprintf(stderr, " pac2cspac convert PAC to color-space PAC\n");
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29 fprintf(stderr, " stdsw standard SW/NW alignment\n");
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30 fprintf(stderr, "\n");
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31 return 1;
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32 }
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33
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34 int main(int argc, char *argv[])
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35 {
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36 if (argc < 2) return usage();
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37 if (strcmp(argv[1], "fa2pac") == 0) return bwa_fa2pac(argc-1, argv+1);
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38 else if (strcmp(argv[1], "pac2bwt") == 0) return bwa_pac2bwt(argc-1, argv+1);
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39 else if (strcmp(argv[1], "pac2bwtgen") == 0) return bwt_bwtgen_main(argc-1, argv+1);
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40 else if (strcmp(argv[1], "bwtupdate") == 0) return bwa_bwtupdate(argc-1, argv+1);
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41 else if (strcmp(argv[1], "pac_rev") == 0) return bwa_pac_rev(argc-1, argv+1);
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42 else if (strcmp(argv[1], "bwt2sa") == 0) return bwa_bwt2sa(argc-1, argv+1);
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43 else if (strcmp(argv[1], "index") == 0) return bwa_index(argc-1, argv+1);
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44 else if (strcmp(argv[1], "aln") == 0) return bwa_aln(argc-1, argv+1);
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45 else if (strcmp(argv[1], "sw") == 0) return bwa_stdsw(argc-1, argv+1);
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46 else if (strcmp(argv[1], "samse") == 0) return bwa_sai2sam_se(argc-1, argv+1);
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47 else if (strcmp(argv[1], "sampe") == 0) return bwa_sai2sam_pe(argc-1, argv+1);
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48 else if (strcmp(argv[1], "pac2cspac") == 0) return bwa_pac2cspac(argc-1, argv+1);
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49 else if (strcmp(argv[1], "stdsw") == 0) return bwa_stdsw(argc-1, argv+1);
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50 else if (strcmp(argv[1], "bwtsw2") == 0) return bwa_bwtsw2(argc-1, argv+1);
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51 else if (strcmp(argv[1], "dbwtsw") == 0) return bwa_bwtsw2(argc-1, argv+1);
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52 else if (strcmp(argv[1], "bwasw") == 0) return bwa_bwtsw2(argc-1, argv+1);
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53 else {
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54 fprintf(stderr, "[main] unrecognized command '%s'\n", argv[1]);
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55 return 1;
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56 }
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57 return 0;
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58 }
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