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comparison gene_fraction/src/Sam.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 SAM_H
2 #define SAM_H
3
4 #include <string>
5 #include <vector>
6
7 #include "args.h"
8 #include "Alignments.h"
9
10 /**
11 * Class for dealing with sam files
12 */
13
14 class Sam {
15 public:
16 /**
17 * Ctor initializes sam file path
18 */
19 Sam(std::string sam_fp);
20 void read_sam(cmd_args args);
21
22 /**
23 * Reads sam file from stdin
24 */
25 void read_from_stdin();
26
27 /**
28 * Reads sam file from directory or file path
29 */
30 void read_from_file(const std::string &sam_fp);
31
32 /**
33 *
34 */
35 void read_from_dir(const std::string &sam_dir_fp);
36
37 std::vector<Alignments> alignment;
38
39 private:
40 std::string _sam_fp;
41 };
42
43
44
45
46
47 #endif /* SAM_H */
48