1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
|
package driver;
import java.io.File;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Collections;
import fileIO.ReadWrite;
import fileIO.TextFile;
import fileIO.TextStreamWriter;
import shared.Parse;
import shared.Parser;
import shared.PreParser;
import shared.Shared;
import shared.Tools;
/**
* @author Brian Bushnell
* @date Nov 21, 2014
*
*/
public class CorrelateIdentity {
/*--------------------------------------------------------------*/
/*---------------- Initialization ----------------*/
/*--------------------------------------------------------------*/
/**
* Code entrance from the command line.
* @param args Command line arguments
*/
public static void main(String[] args){
//Create a new CorrelateIdentity instance
CorrelateIdentity x=new CorrelateIdentity(args);
///And run it
x.process();
//Close the print stream if it was redirected
Shared.closeStream(outstream);
}
/**
* Constructor.
* @param args Command line arguments
*/
public CorrelateIdentity(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
/* Set global defaults */
ReadWrite.ZIPLEVEL=6;
ReadWrite.USE_UNPIGZ=true;
ReadWrite.USE_PIGZ=true;
/* Parse arguments */
for(int i=0; i<args.length; i++){
final String arg=args[i];
String[] split=arg.split("=");
String a=split[0].toLowerCase();
String b=split.length>1 ? split[1] : null;
if(Parser.parseZip(arg, a, b)){
//do nothing
}else if(Parser.parseQuality(arg, a, b)){
//do nothing
}else if(a.equals("in") || a.equals("in1")){
in1=b;
}else if(a.equals("in2")){
in2=b;
}else if(a.equals("out") || a.equals("out1")){
out=b;
}else if(a.equals("samplerate")){
samplerate=Float.parseFloat(b);
assert(samplerate<=1f && samplerate>=0f) : "samplerate="+samplerate+"; should be between 0 and 1";
}else if(a.equals("sampleseed")){
sampleseed=Long.parseLong(b);
}else if(a.equals("overwrite") || a.equals("ow")){
overwrite=Parse.parseBoolean(b);
}else{
throw new RuntimeException("Unknown parameter "+args[i]);
}
}
{//Process parser fields
Parser.processQuality();
}
if(!Tools.testOutputFiles(overwrite, append, false, out)){
throw new RuntimeException("\nCan't write to some output files; overwrite="+overwrite+"\n");
}
if(!Tools.testInputFiles(false, true, in1, in2)){
throw new RuntimeException("\nCan't read some input files.\n");
}
if(!Tools.testForDuplicateFiles(true, in1, in2, out)){
throw new RuntimeException("\nSome file names were specified multiple times.\n");
}
assert(in1==null || in1.toLowerCase().startsWith("stdin") || in1.toLowerCase().startsWith("standardin") || new File(in1).exists()) : "Can't find "+in1;
}
/*--------------------------------------------------------------*/
/*---------------- Outer Methods ----------------*/
/*--------------------------------------------------------------*/
public void process(){
final String[][] matrix1, matrix2;
{
TextFile tf=new TextFile(in1);
String[] s=tf.toStringLines();
tf.close();
matrix1=tf.doublesplitWhitespace(s, true);
}
{
TextFile tf=new TextFile(in2);
String[] s=tf.toStringLines();
tf.close();
matrix2=tf.doublesplitWhitespace(s, true);
}
ArrayList<String[]> list=new ArrayList<String[]>();
for(int i=0; i<matrix1.length; i++){
for(int j=1; j<=i; j++){
list.add(new String[] {matrix1[i][j], matrix2[i][j]});
}
}
Collections.shuffle(list);
TextStreamWriter tsw=new TextStreamWriter(out, overwrite, append, true);
tsw.start();
for(String[] pair : list){
tsw.print(pair[0]+"\t"+pair[1]+"\n");
}
tsw.poisonAndWait();
}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
/** Input files */
public String in1, in2;
/** Output file */
public String out;
// private Random randy=new Random();
private float samplerate=1;
private float sampleseed=-1;
private int columnLength=Integer.MAX_VALUE;
private boolean overwrite=true;
private boolean append=false;
/*--------------------------------------------------------------*/
/*---------------- Static Fields ----------------*/
/*--------------------------------------------------------------*/
/** Verbose messages */
public static final boolean verbose=false; //123
/** Print messages to this stream */
private static PrintStream outstream=System.err;
}
|
