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annotate gene_fraction/src/Sam.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 SAM_H
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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2 #define SAM_H
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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4 #include <string>
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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5 #include <vector>
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7 #include "args.h"
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8 #include "Alignments.h"
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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10 /**
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11 * Class for dealing with sam files
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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12 */
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14 class Sam {
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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15 public:
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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16 /**
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17 * Ctor initializes sam file path
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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18 */
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19 Sam(std::string sam_fp);
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20 void read_sam(cmd_args args);
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22 /**
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23 * Reads sam file from stdin
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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24 */
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25 void read_from_stdin();
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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27 /**
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28 * Reads sam file from directory or file path
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29 */
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30 void read_from_file(const std::string &sam_fp);
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32 /**
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33 *
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34 */
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35 void read_from_dir(const std::string &sam_dir_fp);
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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37 std::vector<Alignments> alignment;
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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39 private:
2aad8349d84b planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5
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40 std::string _sam_fp;
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41 };
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47 #endif /* SAM_H */
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