--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/rDiff/mex/read.h	Thu Feb 14 23:38:36 2013 -0500
@@ -0,0 +1,72 @@
+/*
+*  This program is free software; you can redistribute it and/or modify
+*  it under the terms of the GNU General Public License as published by
+*  the Free Software Foundation; either version 3 of the License, or
+*  (at your option) any later version.
+*
+*   Written (W) 2010-2011 Jonas Behr, Regina Bohnert, Gunnar Raetsch
+*   Copyright (C) 2010-2011 Max Planck Society
+*/
+
+
+#ifndef __READ_H__
+#define __READ_H__
+
+#include <stdint.h>
+#include <cctype>
+#include <stdio.h>
+#include <vector>
+  using std::vector;
+
+
+class CRead {   
+ public:
+  /** constructor
+   */
+  CRead();
+  ~CRead();
+  
+  vector<int> block_starts;
+  vector<int> block_lengths;
+  char* read_id;
+  char* sam_line;
+  int start_pos;
+  char * strand;
+  int matches;
+  int mismatches;
+  int multiple_alignment_index;
+  bool left; 
+  bool right;
+  bool reverse;
+  
+  void get_coverage(int p_start_pos, int p_end_pos, uint32_t* coverage);
+  int get_last_position();
+  void get_reads_sparse(int p_start_pos, int p_end_pos, double* reads, uint32_t & reads_c, uint32_t row_idx);
+  void get_introns(vector<int>* introns);
+  void get_introns(vector<uint32_t>* intron_starts, vector<uint32_t>* intron_ends, vector<uint32_t>* block_len1, vector<uint32_t>* block_len2); 
+  void get_acc_splice_sites(vector<int>* acc_pos);
+  void get_don_splice_sites(vector<int>* acc_pos);
+  int max_intron_len();
+  int min_exon_len();
+  bool operator==(const CRead& read) const;
+  void print();
+  void set_strand(char s);
+  int get_mismatches();
+  static bool compare_by_read_id(const CRead* read1, const CRead* read2)
+  {
+	if (!read1->read_id)
+		return true;
+	if (!read2->read_id)
+		return false;
+
+	int cnt1=0;
+	while (read1->read_id[cnt1]!='\0')
+		cnt1++;
+	int cnt2 = 0;
+	while (read2->read_id[cnt2]!='\0')
+		cnt2++;
+	
+	return std::lexicographical_compare(read1->read_id,read1->read_id+cnt1,read2->read_id,read2->read_id+cnt2);
+  };
+};
+#endif