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package jgi;
import java.io.PrintStream;
import dna.AminoAcid;
import fileIO.ByteFile1;
import fileIO.ByteFile2;
import fileIO.ByteStreamWriter;
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.ConcurrentGenericReadInputStream;
import stream.FASTQ;
import stream.FastaReadInputStream;
import structures.ByteBuilder;
import tracker.ReadStats;
/**
* @author Brian Bushnell
* @date Oct 17, 2014
*
*/
public class MakePolymers {
public static void main(String[] args){
Timer t=new Timer();
MakePolymers x=new MakePolymers(args);
x.process(t);
//Close the print stream if it was redirected
Shared.closeStream(x.outstream);
}
public MakePolymers(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
Shared.capBuffers(4);
ReadWrite.USE_PIGZ=ReadWrite.USE_UNPIGZ=true;
ReadWrite.setZipThreads(Shared.threads());
FASTQ.TEST_INTERLEAVED=FASTQ.FORCE_INTERLEAVED=false;
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(a.equals("verbose")){
verbose=Parse.parseBoolean(b);
ByteFile1.verbose=verbose;
ByteFile2.verbose=verbose;
stream.FastaReadInputStream.verbose=verbose;
ConcurrentGenericReadInputStream.verbose=verbose;
stream.FastqReadInputStream.verbose=verbose;
ReadWrite.verbose=verbose;
}else if(a.equals("k")){
mink=maxk=Integer.parseInt(b);
}else if(a.equals("mink")){
mink=Integer.parseInt(b);
}else if(a.equals("maxk")){
maxk=Integer.parseInt(b);
}else if(a.equals("len") || a.equals("minlen")){
minLen=Integer.parseInt(b);
}else if(parser.parse(arg, a, b)){
//do nothing
}else{
outstream.println("Unknown parameter "+args[i]);
assert(false) : "Unknown parameter "+args[i];
// throw new RuntimeException("Unknown parameter "+args[i]);
}
}
{//Process parser fields
Parser.processQuality();
overwrite=ReadStats.overwrite=parser.overwrite;
append=ReadStats.append=parser.append;
out1=parser.out1;
}
assert(FastaReadInputStream.settingsOK());
if(out1!=null && out1.equalsIgnoreCase("null")){out1=null;}
if(!Tools.testOutputFiles(overwrite, append, false, out1)){
outstream.println((out1==null)+", "+out1);
throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out1+"\n");
}
ffout1=FileFormat.testOutput(out1, FileFormat.FASTA, null, true, overwrite, append, false);
}
void process(Timer t){
final ByteStreamWriter bsw;
if(ffout1!=null){
bsw=new ByteStreamWriter(ffout1);
bsw.start();
}else{bsw=null;}
for(int i=mink; i<=maxk; i++){
writeSequence(i, bsw);
}
if(bsw!=null){errorState|=bsw.poisonAndWait();}
t.stop();
outstream.println(Tools.timeReadsBasesProcessed(t, readsProcessed, basesProcessed, 8));
if(errorState){
throw new RuntimeException(getClass().getName()+" terminated in an error state; the output may be corrupt.");
}
}
private void writeSequence(int k, ByteStreamWriter bsw){
ByteBuilder bb=new ByteBuilder();
final int minLen2=((minLen+k-1)/k)*k;
final int minCount;
if(minLen2-minLen>=k-1){
minCount=minLen2/k;
}else{
minCount=minLen2/k+1;
}
final long max=(1<<(2*k))-1;
for(long kmer=0; kmer<=max; kmer++){
bb.append('>').append(k).append('_').append(kmer).append('\n');
for(int i=0; i<minCount; i++){
basesProcessed+=k;
toBytes(kmer, k, bb);
}
readsProcessed++;
bb.nl();
if(bb.length>=16384){
bsw.print(bb);
bb.clear();
}
}
if(bb.length>0){
bsw.print(bb);
bb.clear();
}
}
public static final void toBytes(long kmer, int k, ByteBuilder bb){
for(int i=k-1; i>=0; i--){
int x=(int)((kmer>>(2*i))&3);
bb.append(AminoAcid.numberToBase[x]);
}
}
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
private long readsProcessed=0;
private long basesProcessed=0;
private int mink=1, maxk=1;
private int minLen=31;
private String out1=null;
private final FileFormat ffout1;
/*--------------------------------------------------------------*/
private PrintStream outstream=System.err;
public static boolean verbose=false;
public boolean errorState=false;
private boolean overwrite=true;
private boolean append=false;
}
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