--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_fraction/src/Alignments.h	Sun Feb 21 23:31:55 2016 -0500
@@ -0,0 +1,68 @@
+#ifndef ALIGNMENTS_H
+#define ALIGNMENTS_H
+
+#include <string>
+#include <vector>
+
+/**
+ * Stores information about an alignment
+ */
+struct alignment_fields {
+    std::string QNAME;
+    int FLAG;
+    std::string RNAME;
+    int POS;
+    int MAPQ;
+    std::string CIGAR;
+    std::string RNEXT;
+    int PNEXT;
+    int TLEN;
+    std::string SEQ;
+    std::string QUAL;
+};
+
+/**
+ * Class for dealing with alignments
+ */
+class Alignments {
+public:
+	/**
+ 	 * Ctor that initializes alignment
+ 	 */ 
+	Alignments(std::string alignment);
+
+	/**
+ 	 * Stores information about each of the eleven
+ 	 * required alignment fields
+ 	 */ 
+    	void fill_alignment_fields(const std::string &alignment);
+
+    	std::vector<std::pair<int,char>> cigar();
+
+	inline std::string alignment() const	    { return _alignment;  };
+
+    	inline std::string qname() const            { return field.QNAME; };
+    	inline std::string rname() const            { return field.RNAME; };
+    	inline std::string cigar() const            { return field.CIGAR; };
+    	inline std::string rnext() const            { return field.RNEXT; };
+    	inline std::string seq() const              { return field.SEQ;   };
+    	inline std::string qual() const             { return field.QUAL;  };
+
+    	inline int flag() const                     { return field.FLAG;  };
+    	inline int pos() const                      { return field.POS;   };
+    	inline int mapq() const                     { return field.MAPQ;  };
+    	inline int pnext() const                    { return field.PNEXT; };
+    	inline int tlen() const			    { return field.TLEN;  };
+
+private:
+	/**
+         * Returns a pair of cigar operations as (occurrence, operation)
+         * Ex: 10M5I -> (10, M), (5, I)
+         */
+    	std::vector<std::pair<int,char>> get_cigar_operations(const std::string &cigar);
+
+    	std::string _alignment;
+    	alignment_fields field;
+};
+
+#endif /* ALIGNMENTS_H */