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comparison gene_fraction/src/args.h @ 0:f95150c37d38 draft default tip

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planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
author chrisd
date Sun, 21 Feb 2016 23:31:55 -0500
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-1:000000000000 0:f95150c37d38
1 #ifndef ARGS_H
2 #define ARGS_H
3
4 #include "int_util.h"
5
6 #include <string>
7 #include <vector>
8 #include <list>
9
10 static void usage() {
11 fprintf(stderr, "\n");
12 fprintf(stderr, "Program: Coverage Sampler \n");
13 fprintf(stderr, "Contact: Chris Dean <cdean11@rams.colostate.edu\n\n");
14 fprintf(stderr, "Usage: csa [options]\n\n");
15 fprintf(stderr, "Options:\n\n");
16 fprintf(stderr, " -amr_fp amr database path\n");
17 fprintf(stderr, " -sam_fp sam file path\n");
18 fprintf(stderr, " -min starting level\n");
19 fprintf(stderr, " -max ending level\n");
20 fprintf(stderr, " -skip amount of levels to skip\n");
21 fprintf(stderr, " -t gene fraction threshold\n");
22 fprintf(stderr, " -samples amount of samples per level\n");
23 fprintf(stderr, " -d directory parsing\n");
24 fprintf(stderr, " -bam bam file parsing\n");
25 fprintf(stderr, " -out_fp output file path\n\n");
26 }
27
28 /**
29 * Encapsulates information input
30 * from the command line.
31 */
32 struct cmd_args {
33 std::string amr_fp;
34 std::string sam_fp;
35 std::list<std::string> sam_dir_fp;
36 std::string out_fp;
37
38 int threshold;
39 int min;
40 int max;
41 int skip;
42 int s_per_lev;
43
44 bool sam_dir = false; /* This will be set to true when parsing a
45 directory of sam files. */
46 bool bam_stream = false; /* This will be set to true when executing
47 samtools view -h example.bam | csa > output
48 from the command line. */
49 };
50
51 /**
52 * Returns a struct of command line arguments.
53 */
54 static inline cmd_args
55 parse_command_line(int argc, char *argv[]) {
56 std::vector<std::string> args(argv, argv + argc);
57
58 cmd_args arg;
59
60 for(int i = 1; i < argc; i++) {
61 if(args[i].compare("-amr_fp") == 0)
62 arg.amr_fp = args[++i];
63 else if(args[i].compare("-sam_fp") == 0)
64 arg.sam_fp = args[++i];
65 else if(args[i].compare("-out_fp") == 0)
66 arg.out_fp = args[++i];
67 else if(args[i].compare("-t") == 0)
68 arg.threshold = s_to_i(args[++i]);
69 else if(args[i].compare("-min") == 0)
70 arg.min = s_to_i(args[++i]);
71 else if(args[i].compare("-max") == 0)
72 arg.max = s_to_i(args[++i]);
73 else if(args[i].compare("-skip") == 0)
74 arg.skip = s_to_i(args[++i]);
75 else if(args[i].compare("-samples") == 0)
76 arg.s_per_lev = s_to_i(args[++i]);
77 else if(args[i].compare("-d") == 0)
78 arg.sam_dir = true;
79 else if(args[i].compare("-bam") == 0)
80 arg.bam_stream = true;
81 else {
82 usage();
83 exit(EXIT_FAILURE);
84 }
85 }
86
87 return arg;
88 }
89
90 #endif /* ARGS_H */