Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/icecream/IceCreamGrader.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
1 package icecream;
2
3 import java.io.File;
4 import java.io.PrintStream;
5 import java.util.ArrayList;
6
7 import fileIO.ByteFile;
8 import fileIO.ByteFile1;
9 import fileIO.ByteFile2;
10 import fileIO.FileFormat;
11 import fileIO.ReadWrite;
12 import shared.Parse;
13 import shared.Parser;
14 import shared.PreParser;
15 import shared.ReadStats;
16 import shared.Shared;
17 import shared.Timer;
18 import shared.Tools;
19 import stream.ConcurrentGenericReadInputStream;
20 import stream.ConcurrentReadInputStream;
21 import stream.FASTQ;
22 import stream.FastaReadInputStream;
23 import stream.Read;
24 import stream.SamLine;
25 import structures.ListNum;
26
27 /**
28 * @author Brian Bushnell
29 * @date June 11, 2019
30 *
31 */
32 public class IceCreamGrader {
33
34 public static void main(String[] args){
35 //Start a timer immediately upon code entrance.
36 Timer t=new Timer();
37
38 //Create an instance of this class
39 IceCreamGrader x=new IceCreamGrader(args);
40
41 //Run the object
42 x.process(t);
43
44 //Close the print stream if it was redirected
45 Shared.closeStream(x.outstream);
46 }
47
48 public IceCreamGrader(String[] args){
49
50 {//Preparse block for help, config files, and outstream
51 PreParser pp=new PreParser(args, getClass(), false);
52 args=pp.args;
53 outstream=pp.outstream;
54 }
55
56 //Set shared static variables
57 Shared.capBuffers(4); //Only for singlethreaded programs
58 ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
59 ReadWrite.MAX_ZIP_THREADS=Shared.threads();
60 FASTQ.TEST_INTERLEAVED=FASTQ.FORCE_INTERLEAVED=false;
61 SamLine.SET_FROM_OK=true;
62
63 Parser parser=new Parser();
64 for(int i=0; i<args.length; i++){
65 String arg=args[i];
66 String[] split=arg.split("=");
67 String a=split[0].toLowerCase();
68 String b=split.length>1 ? split[1] : null;
69 if(b!=null && b.equalsIgnoreCase("null")){b=null;}
70
71 if(a.equals("verbose")){
72 verbose=Parse.parseBoolean(b);
73 ByteFile1.verbose=verbose;
74 ByteFile2.verbose=verbose;
75 stream.FastaReadInputStream.verbose=verbose;
76 ConcurrentGenericReadInputStream.verbose=verbose;
77 stream.FastqReadInputStream.verbose=verbose;
78 ReadWrite.verbose=verbose;
79 }else if(parser.parse(arg, a, b)){
80 //do nothing
81 }
82
83 else if(parser.in1==null && i==0 && !arg.contains("=") && (arg.toLowerCase().startsWith("stdin") || new File(arg).exists())){
84 parser.in1=arg;
85 }else if(parser.out1==null && i==1 && !arg.contains("=")){
86 parser.out1=arg;
87 }else{
88 outstream.println("Unknown parameter "+args[i]);
89 assert(false) : "Unknown parameter "+args[i];
90 // throw new RuntimeException("Unknown parameter "+args[i]);
91 }
92 }
93
94 {//Process parser fields
95 Parser.processQuality();
96
97 maxReads=parser.maxReads;
98
99 overwrite=ReadStats.overwrite=parser.overwrite;
100 append=ReadStats.append=parser.append;
101
102 in1=parser.in1;
103
104 extin=parser.extin;
105 }
106
107 assert(FastaReadInputStream.settingsOK());
108
109 if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
110 if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2){
111 ByteFile.FORCE_MODE_BF2=false;
112 ByteFile.FORCE_MODE_BF1=true;
113 }
114
115 ffin1=FileFormat.testInput(in1, FileFormat.FASTQ, extin, true, true);
116 }
117
118 void process(Timer t){
119
120 final ConcurrentReadInputStream cris;
121 {
122 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null);
123 cris.start();
124 if(verbose){outstream.println("Started cris");}
125 }
126
127 long readsProcessed=0, readsOut=0;
128 long basesProcessed=0, basesOut=0;
129
130 {
131
132 ListNum<Read> ln=cris.nextList();
133 ArrayList<Read> reads=(ln!=null ? ln.list : null);
134
135 // outstream.println("Fetched "+reads);
136
137 if(reads!=null && !reads.isEmpty()){
138 Read r=reads.get(0);
139 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired());
140 }
141
142 while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
143
144 final ArrayList<Read> listOut=new ArrayList<Read>(reads.size());
145 for(int idx=0; idx<reads.size(); idx++){
146 final Read r1=reads.get(idx);
147
148 final int initialLength1=r1.length();
149 final boolean keep=process(r1);
150 if(keep){
151 listOut.add(r1);
152 readsOut++;
153 basesOut+=r1.length();
154 }
155
156 readsProcessed++;
157 basesProcessed+=initialLength1;
158 }
159
160 cris.returnList(ln);
161 ln=cris.nextList();
162 reads=(ln!=null ? ln.list : null);
163 }
164 if(ln!=null){
165 cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
166 }
167 }
168
169 errorState|=ReadStats.writeAll();
170
171 errorState|=ReadWrite.closeStreams(cris);
172
173 t.stop();
174 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
175 // outstream.println(Tools.readsBasesOut(readsProcessed, basesProcessed, readsOut, basesOut, 8, false));
176 outstream.println();
177 outstream.println(Tools.numberPercent("Good Reads:", goodReads, goodReads*100.0/readsProcessed, 3, 8));
178 outstream.println(Tools.numberPercent("Good Bases:", goodBases, goodBases*100.0/basesProcessed, 3, 8));
179 outstream.println(Tools.numberPercent("Bad Reads:", badReads, badReads*100.0/readsProcessed, 3, 8));
180 outstream.println(Tools.numberPercent("Bad Bases:", badBases, badBases*100.0/basesProcessed, 3, 8));
181
182 if(errorState){
183 throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
184 }
185 }
186
187 /*--------------------------------------------------------------*/
188
189 private boolean process(Read r){
190 boolean iceCream=ReadBuilder.isIceCream(r.id);
191 if(iceCream){
192 badReads++;
193 badBases+=r.length();
194 }else{
195 goodReads++;
196 goodBases+=r.length();
197 }
198 return true;
199 }
200
201 /*--------------------------------------------------------------*/
202
203 private String in1=null;
204
205 private String extin=null;
206
207 /*--------------------------------------------------------------*/
208
209 private long maxReads=-1;
210
211 private long goodReads=0;
212 private long goodBases=0;
213 private long badReads=0;
214 private long badBases=0;
215
216 /*--------------------------------------------------------------*/
217
218 private final FileFormat ffin1;
219
220
221 /*--------------------------------------------------------------*/
222
223 private PrintStream outstream=System.err;
224 public static boolean verbose=false;
225 public boolean errorState=false;
226 private boolean overwrite=false;
227 private boolean append=false;
228
229 }