Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/clump/StreamToOutput.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 clump;
2
3 import java.io.File;
4 import java.io.IOException;
5 import java.util.ArrayList;
6
7 import fileIO.FileFormat;
8 import fileIO.ReadWrite;
9 import sort.SortByName;
10 import stream.ConcurrentReadInputStream;
11 import stream.ConcurrentReadOutputStream;
12 import stream.Read;
13 import structures.ListNum;
14
15 public class StreamToOutput {
16
17 public StreamToOutput(FileFormat ffin1, FileFormat ffin2, ConcurrentReadOutputStream[] rosa_, KmerComparator old, boolean sortByName_, boolean incrementComparator){
18 final ConcurrentReadInputStream cris=ConcurrentReadInputStream.getReadInputStream(-1, false, ffin1, ffin2, null, null);
19 cris.start();
20 rosa=rosa_;
21 kc=(incrementComparator ? new KmerComparator(old.k, old.seed+1, old.border-1, old.hashes, false, false) : old);
22 sortByName=sortByName_;
23 }
24
25 public StreamToOutput(ConcurrentReadInputStream cris_, ConcurrentReadOutputStream[] rosa_, KmerComparator old, boolean sortByName_, boolean incrementComparator){
26 cris=cris_;
27 rosa=rosa_;
28 kc=(incrementComparator ? new KmerComparator(old.k, old.seed+1, old.border-1, old.hashes, false, false) : old);
29 sortByName=sortByName_;
30 }
31
32 public boolean process(){
33 if(rosa==null || rosa.length==0){return errorState;}
34
35 File temp=null;
36 if(sortByName){
37 try {
38 temp=File.createTempFile("temp_namesort_", ".fq.gz");
39 } catch (IOException e) {
40 // TODO Auto-generated catch block
41 e.printStackTrace();
42 }
43 SortByName sbn=new SortByName(new String[] {"out="+temp.getAbsolutePath()});
44 sbn.processInner(cris);
45 FileFormat ff=FileFormat.testInput(temp.getAbsolutePath(), null, false);
46 cris=ConcurrentReadInputStream.getReadInputStream(-1, false, ff, null, null, null);
47 }
48
49 if(rosa.length==1){
50 processSingle(cris);
51 }else{
52 processMulti(cris);
53 }
54
55 errorState|=ReadWrite.closeStream(cris);
56 if(temp!=null){
57 temp.delete();
58 }
59 return errorState;
60 }
61
62 public void processSingle(ConcurrentReadInputStream cris){
63
64 ListNum<Read> ln=cris.nextList();
65 ArrayList<Read> reads=(ln!=null ? ln.list : null);
66
67 while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
68 if(rosa!=null){rosa[0].add(reads, ln.id);}
69
70 for(Read r : reads){
71 readsIn+=r.pairCount();
72 basesIn+=r.pairLength();
73 }
74
75 cris.returnList(ln);
76
77 ln=cris.nextList();
78 reads=(ln!=null ? ln.list : null);
79 }
80
81 if(ln!=null){
82 cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
83 }
84 }
85
86 public void processMulti(ConcurrentReadInputStream cris){
87 final int groups=rosa.length;
88
89 @SuppressWarnings("unchecked")
90 final ArrayList<Read>[] out=new ArrayList[groups];
91 for(int i=0; i<out.length; i++){
92 out[i]=new ArrayList<Read>();
93 }
94
95 ListNum<Read> ln=cris.nextList();
96 ArrayList<Read> reads=(ln!=null ? ln.list : null);
97
98 while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
99 for(Read r : reads){
100 long kmer=kc.hash(r, null, 0, false);
101 int group=(int)(kmer%groups);
102 out[group].add(r);
103
104 readsIn+=r.pairCount();
105 basesIn+=r.pairLength();
106 }
107 for(int group=0; group<groups; group++){
108 rosa[group].add(out[group], ln.id);
109 out[group]=new ArrayList<Read>();
110 }
111
112 cris.returnList(ln);
113
114 ln=cris.nextList();
115 reads=(ln!=null ? ln.list : null);
116 }
117
118 if(ln!=null){
119 cris.returnList(ln.id, ln.list==null || ln.list.isEmpty());
120 }
121 }
122
123 long readsIn=0;
124 long basesIn=0;
125
126 // final FileFormat ffin1;
127 // final FileFormat ffin2;
128 ConcurrentReadInputStream cris;
129 ConcurrentReadOutputStream[] rosa;
130 final KmerComparator kc;
131 final boolean sortByName;
132
133 boolean errorState=false;
134
135 }