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comparison NGSrich_0.5.5/src/datastructures/ReadLine.java @ 0:89ad0a9cca52 default tip

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author pfrommolt
date Mon, 21 Nov 2011 08:12:19 -0500
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-1:000000000000 0:89ad0a9cca52
1 package datastructures;
2
3 import java.util.Scanner;
4
5 /**
6 * Represents a read line from the read alignment file.
7 *
8 * @author Ali Abdallah
9 * @version 03.08.2011
10 * @since Java 1.6
11 */
12
13 public class ReadLine implements Line {
14
15 String
16 /**
17 * Query (pair) name.
18 */
19 name,
20 /**
21 * Reference sequence name.
22 */
23 chrom;
24 /**
25 * Start position of the read.
26 */
27 int start,
28 /**
29 * End Position of the read.
30 */
31 end,
32 /**
33 * Length of the read.
34 */
35 length;
36
37 public ReadLine(String line){
38 // line format:
39 // qname flag rname pos mapq cigar mrnm mpos isize seq qual tag
40 Scanner s = new Scanner(line);
41 name = s.next();
42 s.next();
43 chrom = s.next();
44 start = s.nextInt();
45 s.next(); s.next();s.next();s.next();s.next();
46 length = s.next().length();
47 end = start+length-1;
48 }
49
50 public String name(){
51 return name;
52 }
53
54 public String chrom() {
55 return chrom;
56 }
57
58 public int end() {
59 return end;
60 }
61
62 public int start() {
63 return start;
64 }
65
66 public int length(){
67 return length;
68 }
69
70 public String toString(){
71 return name+"\t"+chrom+"\t"+start+"\t"+end;
72 }
73 }