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
|
package template;
import java.util.ArrayList;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import shared.Parse;
import shared.Parser;
import shared.PreParser;
import shared.Shared;
import shared.Timer;
import shared.Tools;
import stream.ConcurrentReadInputStream;
import stream.ConcurrentReadInputStreamD;
import stream.ConcurrentReadOutputStream;
import stream.Read;
import structures.ListNum;
/**
* @author Brian Bushnell
* @date Oct 6, 2014
*
*/
public class A_SampleD {
public static void main(String[] args){
//Start a timer immediately upon code entrance.
Timer t=new Timer();
//Create an instance of this class
A_SampleD x=new A_SampleD(args);
assert(false) : "To support MPI, uncomment this.";
// MPIWrapper.mpiInit(args);
//Run the object
x.process(t);
//Close the print stream if it was redirected
Shared.closeStream(x.outstream);
// MPIWrapper.mpiFinalize();
}
public A_SampleD(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
Parser parser=new Parser();
for(int i=0; i<args.length; i++){
String arg=args[i];
String[] split=arg.split("=");
String a=split[0].toLowerCase();
String b=split.length>1 ? split[1] : null;
if(b!=null && b.equalsIgnoreCase("null")){b=null;}
if(a.equals("verbose")){
verbose=Parse.parseBoolean(b);
ConcurrentReadInputStreamD.verbose=verbose;
}else if(a.equals("parse_flag_goes_here")){
//Set a variable here
}else if(parser.parse(arg, a, b)){
//do nothing
}else{
outstream.println("A_SampleD: Unknown parameter "+args[i]);
assert(false) : "Unknown parameter "+args[i];
// throw new RuntimeException("Unknown parameter "+args[i]);
}
}
{//Process parser fields
Parser.processQuality();
maxReads=parser.maxReads;
in1=parser.in1;
out1=parser.out1;
}
ffout1=FileFormat.testOutput(out1, FileFormat.FASTQ, null, true, true, false, false);
ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, null, true, true);
}
void process(Timer t){
final ConcurrentReadInputStream crisD=ConcurrentReadInputStream.getReadInputStream(
maxReads, false, ffin1, null, Shared.USE_MPI, Shared.MPI_KEEP_ALL);
crisD.start();
final boolean paired=crisD.paired();
final ConcurrentReadOutputStream ros;
if(out1!=null){
final int buff=4;
if(paired && (in1==null || !in1.contains(".sam"))){
outstream.println("A_SampleD: Writing interleaved.");
}
assert(!out1.equalsIgnoreCase(in1) && !out1.equalsIgnoreCase(in1)) : "Input file and output file have same name.";
ros=ConcurrentReadOutputStream.getStream(ffout1, null, buff, null, false);
ros.start();
}else{ros=null;}
long readsProcessed=0;
{
ListNum<Read> ln=crisD.nextList();
ArrayList<Read> reads=(ln!=null ? ln.list : null);
if(verbose){outstream.println("A_SampleD: Initial A_SampleD list: "+(reads==null ? -1 : reads.size()));}
if(reads!=null && !reads.isEmpty()){
Read r=reads.get(0);
assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==crisD.paired());
}
while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
if(verbose){outstream.println("A_SampleD: Fetched "+reads.size()+" reads.");}
for(int idx=0; idx<reads.size(); idx++){
final Read r1=reads.get(idx);
// ********* Process reads here *********
readsProcessed++;
}
if(ros!=null){ros.add(reads, ln.id);}
crisD.returnList(ln.id, ln.list.isEmpty());
if(verbose){outstream.println("A_SampleD: Returned a list.");}
ln=crisD.nextList();
reads=(ln!=null ? ln.list : null);
}
if(ln!=null){
crisD.returnList(ln.id, ln.list==null || ln.list.isEmpty());
}
}
ReadWrite.closeStreams(crisD, ros);
if(verbose){outstream.println("A_SampleD: Finished.");}
t.stop();
outstream.println("A_SampleD: Time: \t"+t);
outstream.println("A_SampleD: Rank "+ Shared.MPI_RANK + ": Reads Processed: "+readsProcessed+" \t"+
Tools.format("%.2fk reads/sec", (readsProcessed/(double)(t.elapsed))*1000000));
}
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
private String in1=null;
private String out1=null;
private final FileFormat ffin1;
private final FileFormat ffout1;
/*--------------------------------------------------------------*/
private long maxReads=-1;
/*--------------------------------------------------------------*/
private java.io.PrintStream outstream=System.err;
public static boolean verbose=false;
}
|
