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1 package datastructures;
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2
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3 import java.util.Scanner;
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4
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5 /**
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6 * Represents a read line from the read alignment file.
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7 *
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8 * @author Ali Abdallah
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9 * @version 03.08.2011
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10 * @since Java 1.6
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11 */
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12
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13 public class ReadLine implements Line {
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14
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15 String
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16 /**
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17 * Query (pair) name.
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18 */
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19 name,
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20 /**
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21 * Reference sequence name.
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22 */
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23 chrom;
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24 /**
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25 * Start position of the read.
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26 */
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27 int start,
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28 /**
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29 * End Position of the read.
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30 */
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31 end,
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32 /**
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33 * Length of the read.
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34 */
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35 length;
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36
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37 public ReadLine(String line){
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38 // line format:
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39 // qname flag rname pos mapq cigar mrnm mpos isize seq qual tag
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40 Scanner s = new Scanner(line);
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41 name = s.next();
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42 s.next();
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43 chrom = s.next();
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44 start = s.nextInt();
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45 s.next(); s.next();s.next();s.next();s.next();
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46 length = s.next().length();
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47 end = start+length-1;
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48 }
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49
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50 public String name(){
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51 return name;
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52 }
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53
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54 public String chrom() {
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55 return chrom;
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56 }
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57
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58 public int end() {
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59 return end;
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60 }
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61
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62 public int start() {
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63 return start;
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64 }
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65
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66 public int length(){
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67 return length;
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68 }
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69
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70 public String toString(){
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71 return name+"\t"+chrom+"\t"+start+"\t"+end;
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72 }
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73 }
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