Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/sketch/InvertKey.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 sketch;
2
3 import java.io.File;
4 import java.io.PrintStream;
5 import java.util.ArrayList;
6
7 import dna.AminoAcid;
8 import fileIO.ByteFile;
9 import fileIO.ByteFile1;
10 import fileIO.ByteFile2;
11 import fileIO.ByteStreamWriter;
12 import fileIO.FileFormat;
13 import fileIO.ReadWrite;
14 import shared.Parse;
15 import shared.Parser;
16 import shared.PreParser;
17 import shared.ReadStats;
18 import shared.Shared;
19 import shared.Timer;
20 import shared.Tools;
21 import stream.ConcurrentGenericReadInputStream;
22 import stream.ConcurrentReadInputStream;
23 import stream.FASTQ;
24 import stream.FastaReadInputStream;
25 import stream.Read;
26 import structures.ListNum;
27 import structures.LongHashSet;
28
29 /**
30 * @author Brian Bushnell
31 * @date Oct 17, 2014
32 *
33 */
34 public class InvertKey extends SketchObject {
35
36 public static void main(String[] args){
37 Timer t=new Timer();
38 InvertKey x=new InvertKey(args);
39 x.process(t);
40
41 //Close the print stream if it was redirected
42 Shared.closeStream(x.outstream);
43 }
44
45 public InvertKey(String[] args){
46
47 {//Preparse block for help, config files, and outstream
48 PreParser pp=new PreParser(args, getClass(), false);
49 args=pp.args;
50 outstream=pp.outstream;
51 }
52
53 Shared.capBuffers(4);
54 ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
55 ReadWrite.MAX_ZIP_THREADS=Shared.threads();
56
57 FASTQ.TEST_INTERLEAVED=FASTQ.FORCE_INTERLEAVED=false;
58 int k_=32, k2_=0;
59
60 Parser parser=new Parser();
61 for(int i=0; i<args.length; i++){
62 String arg=args[i];
63 String[] split=arg.split("=");
64 String a=split[0].toLowerCase();
65 String b=split.length>1 ? split[1] : null;
66
67 if(a.equals("verbose")){
68 verbose=Parse.parseBoolean(b);
69 ByteFile1.verbose=verbose;
70 ByteFile2.verbose=verbose;
71 stream.FastaReadInputStream.verbose=verbose;
72 ConcurrentGenericReadInputStream.verbose=verbose;
73 stream.FastqReadInputStream.verbose=verbose;
74 ReadWrite.verbose=verbose;
75 }else if(a.equals("key")){
76 keyString=b;
77 }else if(a.equals("out")){
78 out1=b;
79 }else if(a.equalsIgnoreCase("k")){
80 assert(b!=null) : "Bad parameter: "+arg;
81 if(b.indexOf(',')>=0){
82 String[] bsplit=b.split(",");
83 assert(bsplit.length==2) : "Bad argument "+arg;
84 int x=Integer.parseInt(bsplit[0]);
85 int y=Integer.parseInt(bsplit[1]);
86 k_=Tools.max(x, y);
87 k2_=Tools.min(x, y);
88 if(k_==k2_){k2_=0;}
89 }else{
90 k_=Integer.parseInt(b);
91 k2_=0;
92 }
93 }else if(a.equalsIgnoreCase("printonce")){
94 printOnce=Parse.parseBoolean(b);
95 }else if(parser.in1==null && i==0 && !arg.contains("=") && (arg.toLowerCase().startsWith("stdin") || new File(arg).exists())){
96 parser.in1=arg;
97 }else if(parser.out1==null && i==1 && !arg.contains("=")){
98 out1=arg;
99 }else if(parser.parse(arg, a, b)){
100 //do nothing
101 }else{
102 outstream.println("Unknown parameter "+args[i]);
103 assert(false) : "Unknown parameter "+args[i];
104 // throw new RuntimeException("Unknown parameter "+args[i]);
105 }
106 }
107
108 k=k_;
109 k2=k2_;
110 shift=2*k;
111 shift2=shift-2;
112 mask=(shift>63 ? -1L : ~((-1L)<<shift)); //Conditional allows K=32
113
114 {//Process parser fields
115 Parser.processQuality();
116
117 maxReads=parser.maxReads;
118
119 overwrite=ReadStats.overwrite=parser.overwrite;
120 append=ReadStats.append=parser.append;
121
122 in1=parser.in1;
123 }
124
125 assert(FastaReadInputStream.settingsOK());
126
127 if(in1==null){throw new RuntimeException("Error - at least one input file is required.");}
128 if(!ByteFile.FORCE_MODE_BF1 && !ByteFile.FORCE_MODE_BF2){
129 ByteFile.FORCE_MODE_BF2=false;
130 ByteFile.FORCE_MODE_BF1=true;
131 }
132
133 if(out1!=null && out1.equalsIgnoreCase("null")){out1=null;}
134
135 if(!Tools.testOutputFiles(overwrite, append, false, out1)){
136 outstream.println((out1==null)+", "+out1);
137 throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out1+"\n");
138 }
139
140 ffout1=FileFormat.testOutput(out1, FileFormat.FASTA, null, true, overwrite, append, false);
141
142 ffin1=FileFormat.testInput(in1, FileFormat.FASTA, null, true, true);
143
144 SketchObject.postParse();
145
146 if(keyString.indexOf(',')>0){
147 String[] split=keyString.split(",");
148 set=new LongHashSet(split.length*2);
149 for(String s : split){
150 long x=Long.MAX_VALUE-Sketch.parseA48(s);
151 set.add(x);
152 // assert(set.contains(x)) : x+", "+set.size()+", "+set.toStringListView();
153 }
154 key0=-1;
155 // System.err.println(set.toStringListView()+", "+set.size());
156 assert(!set.isEmpty());
157 }else if(keyString.endsWith(".sketch")){
158 SketchTool tool=new SketchTool(10000, 0, false, false);
159 Sketch sk=tool.loadSketchesFromFile(keyString, null, 0, 1000000, SketchObject.ONE_SKETCH, 1f, 0f, 0f, (byte)0, false).get(0);
160 set=new LongHashSet(sk.length()*2);
161 for(long x : sk.keys){set.add(Long.MAX_VALUE-x);}
162 key0=-1;
163 // System.err.println(set.toStringListView()+", "+set.size());
164 assert(!set.isEmpty());
165 }else{
166 key0=Long.MAX_VALUE-Sketch.parseA48(keyString);
167 set=null;
168 // System.err.println(key0);
169 }
170 }
171
172 void process(Timer t){
173
174 final ConcurrentReadInputStream cris;
175 {
176 cris=ConcurrentReadInputStream.getReadInputStream(maxReads, true, ffin1, null, null, null);
177 cris.start();
178 if(verbose){outstream.println("Started cris");}
179 }
180 boolean paired=cris.paired();
181 // if(verbose){
182 if(!ffin1.samOrBam()){outstream.println("Input is being processed as "+(paired ? "paired" : "unpaired"));}
183 // }
184
185 final ByteStreamWriter bsw;
186 if(out1!=null){
187 fasta=ffout1.fasta() && !out1.endsWith(".txt");
188 bsw=new ByteStreamWriter(ffout1);
189 bsw.start();
190 }else{bsw=null;}
191
192 long readsProcessed=0;
193 long basesProcessed=0;
194 boolean finished=false;
195
196 {
197
198 ListNum<Read> ln=cris.nextList();
199 ArrayList<Read> reads=(ln!=null ? ln.list : null);
200
201 // outstream.println("Fetched "+reads);
202
203 if(reads!=null && !reads.isEmpty()){
204 Read r=reads.get(0);
205 assert((ffin1==null || ffin1.samOrBam()) || (r.mate!=null)==cris.paired());
206 }
207
208 while(reads!=null && reads.size()>0 && !finished){
209
210 for(int idx=0; idx<reads.size() && !finished; idx++){
211 final Read r1=reads.get(idx);
212
213 finished=invert(key0, r1, bsw);
214
215 final int initialLength1=r1.length();
216
217 readsProcessed++;
218 basesProcessed+=initialLength1;
219 }
220
221 cris.returnList(ln);
222 ln=cris.nextList();
223 reads=(ln!=null ? ln.list : null);
224 }
225 if(ln!=null){
226 cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
227 }
228 }
229
230 errorState|=(ReadWrite.closeStream(cris));
231 if(bsw!=null){errorState|=bsw.poisonAndWait();}
232
233 t.stop();
234 outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
235
236 if(errorState && !finished && maxReads<1){
237 throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
238 }
239 }
240
241 private boolean invert(long key2, Read r, ByteStreamWriter bsw) {
242 final byte[] bases=r.bases;
243
244 long kmer=0;
245 long rkmer=0;
246 int len=0;
247
248
249 // System.err.println("Looking for "+key+"\t"+Sketch.toA48(key)+"\t"+Sketch.toA48(Long.MAX_VALUE-key));
250
251 for(int i=0; i<bases.length; i++){
252 byte b=bases[i];
253 long x=AminoAcid.baseToNumber[b];
254 long x2=AminoAcid.baseToComplementNumber[b];
255 kmer=((kmer<<2)|x)&mask;
256 rkmer=((rkmer>>>2)|(x2<<shift2))&mask;
257 if(x<0){len=0; rkmer=0;}else{len++;}
258 if(len>=k){
259 kmersProcessed++;
260 final long hashcode=hash(kmer, rkmer);
261 boolean found=(key0>=0 ? hashcode==key0 : set.contains(hashcode));
262 if(found){
263 if(fasta){bsw.println(">"+Sketch.toA48(Long.MAX_VALUE-hashcode)+" "+(i-k+1)+" "+r.id);}
264 bsw.println(AminoAcid.kmerToString(Tools.min(kmer, rkmer), k));
265 if(printOnce){
266 if(key0>=0){return true;}
267 else{
268 set.remove(hashcode);
269 return set.isEmpty();
270 }
271 }
272 }
273 }
274 }
275 return false;
276 }
277
278 /*--------------------------------------------------------------*/
279
280 final long key0;
281 final LongHashSet set;
282
283 final int shift;
284 final int shift2;
285 final long mask;
286
287 boolean printOnce=true;
288 long kmersProcessed=0;
289
290 private String in1=null;
291 boolean fasta;
292 boolean sketch;
293 private String keyString=null;
294
295 private String out1="stdout.fa";
296
297 /*--------------------------------------------------------------*/
298
299 private long maxReads=-1;
300
301 /*--------------------------------------------------------------*/
302
303 private final FileFormat ffin1;
304
305 private final FileFormat ffout1;
306
307
308 /*--------------------------------------------------------------*/
309
310 private PrintStream outstream=System.err;
311 public static boolean verbose=false;
312 public boolean errorState=false;
313 private boolean overwrite=false;
314 private boolean append=false;
315
316 }