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annotate gene_fraction/src/args.h @ 0:2aad8349d84b draft

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planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
author chrisd
date Sun, 21 Feb 2016 23:20:22 -0500
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2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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1 #ifndef ARGS_H
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2 #define ARGS_H
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3
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4 #include "int_util.h"
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5
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6 #include <string>
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7 #include <vector>
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8 #include <list>
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9
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10 static void usage() {
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11 fprintf(stderr, "\n");
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12 fprintf(stderr, "Program: Coverage Sampler \n");
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13 fprintf(stderr, "Contact: Chris Dean <cdean11@rams.colostate.edu\n\n");
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14 fprintf(stderr, "Usage: csa [options]\n\n");
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15 fprintf(stderr, "Options:\n\n");
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16 fprintf(stderr, " -amr_fp amr database path\n");
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17 fprintf(stderr, " -sam_fp sam file path\n");
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18 fprintf(stderr, " -min starting level\n");
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19 fprintf(stderr, " -max ending level\n");
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20 fprintf(stderr, " -skip amount of levels to skip\n");
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21 fprintf(stderr, " -t gene fraction threshold\n");
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22 fprintf(stderr, " -samples amount of samples per level\n");
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23 fprintf(stderr, " -d directory parsing\n");
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24 fprintf(stderr, " -bam bam file parsing\n");
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25 fprintf(stderr, " -out_fp output file path\n\n");
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26 }
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27
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28 /**
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29 * Encapsulates information input
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30 * from the command line.
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31 */
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32 struct cmd_args {
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33 std::string amr_fp;
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34 std::string sam_fp;
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35 std::list<std::string> sam_dir_fp;
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36 std::string out_fp;
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37
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38 int threshold;
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39 int min;
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40 int max;
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41 int skip;
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42 int s_per_lev;
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43
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44 bool sam_dir = false; /* This will be set to true when parsing a
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45 directory of sam files. */
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46 bool bam_stream = false; /* This will be set to true when executing
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47 samtools view -h example.bam | csa > output
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48 from the command line. */
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49 };
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50
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51 /**
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52 * Returns a struct of command line arguments.
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53 */
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54 static inline cmd_args
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55 parse_command_line(int argc, char *argv[]) {
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56 std::vector<std::string> args(argv, argv + argc);
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57
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58 cmd_args arg;
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59
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60 for(int i = 1; i < argc; i++) {
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61 if(args[i].compare("-amr_fp") == 0)
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62 arg.amr_fp = args[++i];
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63 else if(args[i].compare("-sam_fp") == 0)
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64 arg.sam_fp = args[++i];
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65 else if(args[i].compare("-out_fp") == 0)
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66 arg.out_fp = args[++i];
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67 else if(args[i].compare("-t") == 0)
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68 arg.threshold = s_to_i(args[++i]);
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69 else if(args[i].compare("-min") == 0)
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70 arg.min = s_to_i(args[++i]);
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71 else if(args[i].compare("-max") == 0)
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72 arg.max = s_to_i(args[++i]);
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73 else if(args[i].compare("-skip") == 0)
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74 arg.skip = s_to_i(args[++i]);
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75 else if(args[i].compare("-samples") == 0)
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76 arg.s_per_lev = s_to_i(args[++i]);
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77 else if(args[i].compare("-d") == 0)
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78 arg.sam_dir = true;
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79 else if(args[i].compare("-bam") == 0)
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80 arg.bam_stream = true;
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81 else {
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82 usage();
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83 exit(EXIT_FAILURE);
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84 }
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85 }
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86
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87 return arg;
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88 }
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89
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90 #endif /* ARGS_H */