--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/gene_fraction/src/Alignments.cpp	Sun Feb 21 23:31:55 2016 -0500
@@ -0,0 +1,35 @@
+#include "Alignments.h"
+#include "int_util.h"
+
+#include <boost/algorithm/string.hpp>
+
+#include <iostream>
+#include <sstream>
+
+Alignments::Alignments(std::string alignment) : _alignment(alignment) {
+	fill_alignment_fields(alignment);
+}
+
+void Alignments::fill_alignment_fields(const std::string &alignment) {
+	std::istringstream ss(alignment);
+	ss >> field.QNAME >> field.FLAG >> field.RNAME >> field.POS >>
+	      field.MAPQ >> field.CIGAR >> field.RNEXT >> field.PNEXT >>
+	      field.TLEN >> field.SEQ >> field.QUAL;
+}
+
+std::vector<std::pair<int,char>> Alignments::cigar() {
+	return get_cigar_operations(field.CIGAR);
+}
+
+std::vector<std::pair<int,char>> Alignments::get_cigar_operations(const std::string &cigar) {
+	std::vector<std::pair<int,char>> p;
+    	int count;
+    	char operation;
+
+    	std::istringstream ss(cigar);
+    	while(ss >> count >> operation) {
+        	p.push_back(std::make_pair(count, operation));
+    	}
+
+    	return p;
+}