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1 /*
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2 * This program is free software; you can redistribute it and/or modify
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3 * it under the terms of the GNU General Public License as published by
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4 * the Free Software Foundation; either version 3 of the License, or
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5 * (at your option) any later version.
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6 *
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7 * Written (W) 2010-2011 Jonas Behr, Regina Bohnert, Gunnar Raetsch
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8 * Copyright (C) 2010-2011 Max Planck Society
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9 */
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10
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11
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12 #ifndef __READ_H__
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13 #define __READ_H__
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14
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15 #include <stdint.h>
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16 #include <cctype>
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17 #include <stdio.h>
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18 #include <vector>
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19 using std::vector;
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20
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21
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22 class CRead {
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23 public:
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24 /** constructor
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25 */
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26 CRead();
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27 ~CRead();
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28
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29 vector<int> block_starts;
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30 vector<int> block_lengths;
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31 char* read_id;
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32 char* sam_line;
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33 int start_pos;
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34 char * strand;
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35 int matches;
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36 int mismatches;
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37 int multiple_alignment_index;
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38 bool left;
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39 bool right;
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40 bool reverse;
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41
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42 void get_coverage(int p_start_pos, int p_end_pos, uint32_t* coverage);
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43 int get_last_position();
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44 void get_reads_sparse(int p_start_pos, int p_end_pos, double* reads, uint32_t & reads_c, uint32_t row_idx);
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45 void get_introns(vector<int>* introns);
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46 void get_introns(vector<uint32_t>* intron_starts, vector<uint32_t>* intron_ends, vector<uint32_t>* block_len1, vector<uint32_t>* block_len2);
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47 void get_acc_splice_sites(vector<int>* acc_pos);
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48 void get_don_splice_sites(vector<int>* acc_pos);
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49 int max_intron_len();
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50 int min_exon_len();
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51 bool operator==(const CRead& read) const;
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52 void print();
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53 void set_strand(char s);
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54 int get_mismatches();
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55 static bool compare_by_read_id(const CRead* read1, const CRead* read2)
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56 {
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57 if (!read1->read_id)
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58 return true;
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59 if (!read2->read_id)
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60 return false;
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61
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62 int cnt1=0;
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63 while (read1->read_id[cnt1]!='\0')
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64 cnt1++;
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65 int cnt2 = 0;
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66 while (read2->read_id[cnt2]!='\0')
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67 cnt2++;
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68
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69 return std::lexicographical_compare(read1->read_id,read1->read_id+cnt1,read2->read_id,read2->read_id+cnt2);
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70 };
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71 };
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72 #endif
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