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package pacbio;
import java.io.File;
import java.util.ArrayList;
import dna.Data;
import fileIO.FileFormat;
import fileIO.ReadWrite;
import fileIO.TextStreamWriter;
import shared.KillSwitch;
import shared.Parse;
import shared.Parser;
import shared.PreParser;
import shared.Tools;
import stream.ConcurrentLegacyReadInputStream;
import stream.ConcurrentReadInputStream;
import stream.FastaReadInputStream;
import stream.Read;
import stream.SequentialReadInputStream;
import structures.ListNum;
import tracker.ReadStats;
/**
* @author Brian Bushnell
* @date Dec 7, 2012
*
*/
public class MergeReadsAndGenome {
public static void main(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, new Object() { }.getClass().getEnclosingClass(), false);
args=pp.args;
//outstream=pp.outstream;
}
int genome=-1;
String in[]=null;
String out=null;
long reads=-1;
int readlen=300;
boolean overwrite=true;
boolean append=false;
int sequentialOverlap=5;
boolean sequentialStrandAlt=true;
ReadWrite.ZIPLEVEL=2;
FastaReadInputStream.TARGET_READ_LEN=250;
FastaReadInputStream.SPLIT_READS=(FastaReadInputStream.TARGET_READ_LEN>0);
for(int i=0; i<args.length; i++){
final String arg=args[i];
final String[] split=arg.split("=");
String a=split[0].toLowerCase();
String b=split.length>1 ? split[1] : null;
if(Parser.parseCommonStatic(arg, a, b)){
//do nothing
}else if(Parser.parseZip(arg, a, b)){
//do nothing
}else if(Parser.parseFasta(arg, a, b)){
//do nothing
}else if(a.equals("in")){
if("null".equalsIgnoreCase(b)){
//do nothing
}else{
in=b.split(",");
}
}else if(a.equals("out")){
out=b;
}else if(a.equals("build") || a.equals("genome")){
genome=Integer.parseInt(b);
}else 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);
System.out.println("Set overwrite to "+overwrite);
}else if(a.equals("reads")){
reads=Parse.parseKMG(b);
}else if(a.equals("readlen") || a.equals("length") || a.equals("len")){
readlen=Integer.parseInt(b);
}else if(a.equals("sequentialoverlap")){
sequentialOverlap=Integer.parseInt(b);
}else if(a.equals("sequentialstrandalt")){
sequentialStrandAlt=Parse.parseBoolean(b);
}else if(a.equals("verbose")){
verbose=Parse.parseBoolean(b);
}else{
System.err.println("Unknown parameter "+split[i]);
assert(false);
}
}
assert(FastaReadInputStream.settingsOK());
if(in!=null){
File a=new File(out);
for(String s : in){
File b=new File(s);
if(a.equals(b)){throw new RuntimeException("Input file may not equal output file: "+a.toString());}
}
}
assert(out!=null);
TextStreamWriter tsw=new TextStreamWriter(out, overwrite, false, false);
tsw.start();
long id=0;
if(genome>=0){
Data.setGenome(genome);
SequentialReadInputStream.UNLOAD=true;
// SequentialReadInputStream.verbose=true;
SequentialReadInputStream ris=new SequentialReadInputStream(reads, readlen, Tools.max(50, readlen/2), sequentialOverlap, sequentialStrandAlt);
ConcurrentLegacyReadInputStream cris=new ConcurrentLegacyReadInputStream(ris, reads);
cris.start();
id=appendReads(cris, tsw, id);
ReadWrite.closeStream(cris);
}
if(in!=null){
for(String s : in){
final ConcurrentReadInputStream cris;
{
FileFormat ff1=FileFormat.testInput(s, FileFormat.FASTQ, null, true, false);
cris=ConcurrentReadInputStream.getReadInputStream(-1, true, ff1, null);
if(verbose){System.err.println("Started cris");}
cris.start(); //4567
}
id=appendReads(cris, tsw, id);
ReadWrite.closeStream(cris);
}
}
tsw.poisonAndWait();
}
public static long appendReads(ConcurrentReadInputStream cris, TextStreamWriter tsw, long id){
ListNum<Read> ln=cris.nextList();
ArrayList<Read> reads=(ln!=null ? ln.list : null);
while(ln!=null && reads!=null && reads.size()>0){//ln!=null prevents a compiler potential null access warning
for(Read r : reads){
Read b=r.mate;
Read a=correctRead(r, id);
if(a!=null){
tsw.println(a);
id++;
}
b=correctRead(b, id);
if(b!=null){
tsw.println(b);
id++;
}
}
cris.returnList(ln);
//System.err.println("fetching list");
ln=cris.nextList();
reads=(ln!=null ? ln.list : null);
}
if(verbose){System.err.println("Finished reading");}
cris.returnList(ln);
if(verbose){System.err.println("Returned list");}
return id;
}
public static Read correctRead(Read r, long id){
if(r==null){return null;}
r.numericID=id;
r.id=""+id;
if(r.chrom<1){return r;}
int startN=0;
int stopN=r.length()-1;
while(startN<r.length() && r.bases[startN]=='N'){startN++;}
while(stopN>0 && r.bases[stopN]=='N'){stopN--;}
if(startN>0 || stopN<r.length()-1){
if(r.length()-startN-stopN<50){return null;}
r.bases=KillSwitch.copyOfRange(r.bases, startN, stopN+1);
if(r.quality!=null){r.quality=KillSwitch.copyOfRange(r.quality, startN, stopN+1);}
}
return r;
}
public static boolean verbose=false;
}
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