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
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
|
package assemble;
import java.io.File;
import java.io.PrintStream;
import java.util.ArrayList;
import align2.BBMap;
import dna.Data;
import fileIO.ByteFile;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import jgi.FilterByCoverage;
import shared.Parse;
import shared.PreParser;
import shared.Shared;
import shared.Timer;
import shared.Tools;
import tracker.ReadStats;
/**
* @author Brian Bushnell
* @date Jul 8, 2015
*
*/
public class Postfilter {
/**
* Code entrance from the command line.
* @param args Command line arguments
*/
public static void main(String[] args){
Timer t=new Timer();
//Create a new CountKmersExact instance
Postfilter x=new Postfilter(args, true);
///And run it
x.process(t);
//Close the print stream if it was redirected
Shared.closeStream(outstream);
}
/**
* Constructor.
* @param args Command line arguments
*/
public Postfilter(String[] args, boolean setDefaults){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
if(setDefaults){
/* Set global defaults */
ReadWrite.ZIPLEVEL=8;
ReadWrite.USE_UNPIGZ=true;
ReadWrite.USE_PIGZ=true;
if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2 && Shared.threads()>2){
ByteFile.FORCE_MODE_BF2=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(a.equals("append") || a.equals("app")){
append=ReadStats.append=Parse.parseBoolean(b);
}else if(a.equals("overwrite") || a.equals("ow")){
overwrite=Parse.parseBoolean(b);
}else if(a.equals("in") || a.equals("in1")){
in1=b;
}else if(a.equals("in2")){
in2=b;
}else if(a.equals("ref") || a.equals("contigs") || a.equals("assembly")){
ref=b;
}else if(a.equals("out") || a.equals("out1")){
out=b;
}else if(a.equals("outdirty") || a.equals("outd") || a.equals("outbad")){
outdirty=b;
}else if(a.equals("showstats")){
showStats=Parse.parseBoolean(b);
}else if(a.equals("covstats") || a.equals("cov")){
covstats=b;
}else if(a.equals("maxindel")){
maxIndel=Integer.parseInt(b);
}else if(a.equals("minhits")){
minHits=Integer.parseInt(b);
}else if(a.equals("minc") || a.equals("mincov") || a.equals("mincoverage")){
minCoverage=Double.parseDouble(b);
}else if(a.equals("minp") || a.equals("minpercent")){
minCoveredPercent=Double.parseDouble(b);
}else if(a.equals("minr") || a.equals("minreads")){
minReads=Parse.parseKMG(b);
}else if(a.equals("minl") || a.equals("minlen") || a.equals("minlength")){
minLength=Integer.parseInt(b);
}else if(a.equals("rescue")){
rescue=Parse.parseBoolean(b);
}else if(a.equals("trim") || a.equals("trimends")){
if(b==null || Character.isLetter(b.charAt(0))){
trimEnds=Parse.parseBoolean(b) ? 100 : 0;
}else{
trimEnds=Integer.parseInt(b);
}
trimEnds=Tools.max(trimEnds, 0);
}else{
mapArgs.add(arg);
}
}
if(in2==null && in1!=null && in1.contains("#") && !new File(in1).exists()){
in2=in1.replaceFirst("#", "2");
in1=in1.replaceFirst("#", "1");
}
if(!Tools.testOutputFiles(overwrite, append, false, covstats, out)){
throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+
covstats+", "+out+"\n");
}
if(!Tools.testInputFiles(false, true, in1, in2, ref)){
throw new RuntimeException("\nCan't read some input files.\n");
}
if(!Tools.testForDuplicateFiles(true, in1, in2, covstats, out, ref)){
throw new RuntimeException("\nSome file names were specified multiple times.\n");
}
assert(in1!=null);
assert(out!=null);
assert(ref!=null);
assert(covstats!=null);
}
/*--------------------------------------------------------------*/
/*---------------- Outer Methods ----------------*/
/*--------------------------------------------------------------*/
public void process(Timer t){
// bbmap.sh in=../reads.fq.gz ref=contigs.fasta nodisk ambig=all maxindel=100 covstats=covstats.txt minhits=2;
// filterbycoverage.sh in=contigs.fasta out=filtered.fasta cov=covstats.txt mincov=2 minr=6 minp=95 minl=400
mapArgs.add("in="+in1);
if(in2!=null){mapArgs.add("in2="+in2);}
mapArgs.add("ref="+ref);
mapArgs.add("covstats="+covstats);
mapArgs.add("ambig=all");
mapArgs.add("minhits="+minHits);
mapArgs.add("maxindel="+maxIndel);
mapArgs.add("nodisk");
mapArgs.add("append="+append);
mapArgs.add("ow="+overwrite);
mapArgs.add("bw="+bw);
mapArgs.add("tipsearch="+tipsearch);
mapArgs.add("rescue="+rescue);
BBMap.main(mapArgs.toArray(new String[0]));
Data.unloadAll();
mapArgs.clear();
mapArgs.add("in="+ref);
mapArgs.add("out="+out);
if(outdirty!=null){mapArgs.add("outdirty="+outdirty);}
mapArgs.add("covstats="+covstats);
mapArgs.add("mincov="+minCoverage);
mapArgs.add("minr="+minReads);
mapArgs.add("minp="+minCoveredPercent);
mapArgs.add("minl="+minLength);
mapArgs.add("trim="+trimEnds);
mapArgs.add("append="+append);
mapArgs.add("ow="+overwrite);
FilterByCoverage.main(mapArgs.toArray(new String[0]));
if(showStats && out!=null && !FileFormat.isStdio(out)){
outstream.println();
jgi.AssemblyStats2.main(new String[] {"in="+out});
}
}
/*--------------------------------------------------------------*/
/*---------------- Fields ----------------*/
/*--------------------------------------------------------------*/
private ArrayList<String> mapArgs=new ArrayList<String>();
private String in1=null;
private String in2=null;
private String ref=null;
private String out="filtered.fa";
private String outdirty=null;
private String covstats="covstats.txt";
private int maxIndel=0;
private int minHits=2;
private int bw=20;
private int tipsearch=0;
private boolean rescue=false;
private int trimEnds=0;
private double minCoverage=2;
private double minCoveredPercent=95;
private long minReads=6;
private int minLength=400;
boolean showStats=true;
boolean append=false;
boolean overwrite=true;
/*--------------------------------------------------------------*/
/*---------------- Static Fields ----------------*/
/*--------------------------------------------------------------*/
/** Print messages to this stream */
private static PrintStream outstream=System.err;
}
|
