diff gene_fraction/src/Sam.h @ 0:f95150c37d38 draft default tip

planemo upload for repository https://github.com/ChrisD11/Tools commit ddc95e5d6b5f2c0a5340c0bc384aa822db8856d5

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_fraction/src/Sam.h	Sun Feb 21 23:31:55 2016 -0500
@@ -0,0 +1,48 @@
+#ifndef SAM_H
+#define SAM_H
+
+#include <string>
+#include <vector>
+
+#include "args.h"
+#include "Alignments.h"
+
+/**
+ * Class for dealing with sam files
+ */
+
+class Sam {
+public:
+	/**
+ 	 * Ctor initializes sam file path
+ 	 */ 
+	Sam(std::string sam_fp);
+	void read_sam(cmd_args args);
+
+	/**
+ 	 * Reads sam file from stdin 
+ 	 */ 
+	void read_from_stdin();
+
+	/**
+         * Reads sam file from directory or file path
+         */	 
+	void read_from_file(const std::string &sam_fp);
+
+	/**
+ 	 *
+ 	 */	 
+	void read_from_dir(const std::string &sam_dir_fp);
+
+	std::vector<Alignments> alignment;
+
+private:
+	std::string _sam_fp;
+};
+
+
+
+
+
+#endif /* SAM_H */
+