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package align2;
import java.io.PrintStream;
import java.util.ArrayList;
import dna.Data;
import fileIO.TextFile;
import shared.Parse;
import shared.PreParser;
import shared.Shared;
import stream.Read;
/**
* @author Brian Bushnell
* @date Mar 27, 2014
*
*/
public class BBWrap {
public static void main(String[] args){
BBWrap wrapper=new BBWrap();
ArrayList<String> list=wrapper.parse(args);
wrapper.execute(list);
//Close the print stream if it was redirected
Shared.closeStream(outstream);
}
private final ArrayList<String> parse(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
Read.TO_UPPER_CASE=true;
for(int i=0; i<args.length; i++){
final String arg=args[i];
final String[] split=arg.split("=");
final String a=split[0].toLowerCase();
String b=split.length>1 ? split[1] : null;
if(a.equals("path") || a.equals("root")){
Data.setPath(b);
args[i]=null;
}else if(a.equals("mapper")){
mapper=b;
args[i]=null;
}else if(a.equals("ref") || a.equals("reference") || a.equals("fasta")){
ref=b;
args[i]=null;
}else if(a.equals("in") || a.equals("in1")){
add(b, in1List);
args[i]=null;
}else if(a.equals("in2")){
add(b, in2List);
args[i]=null;
}else if(a.equals("inlist") || a.equals("in1list")){
addFileContents(b, in1List);
args[i]=null;
}else if(a.equals("in2list")){
addFileContents(b, in2List);
args[i]=null;
}else if(a.equals("out") || a.equals("out1")){
add(b, out1List);
args[i]=null;
}else if(a.equals("out2")){
add(b, out2List);
args[i]=null;
}else if(a.equals("outlist") || a.equals("out1list")){
addFileContents(b, out1List);
args[i]=null;
}else if(a.equals("out2list")){
addFileContents(b, out2List);
args[i]=null;
}else if(a.equals("outm") || a.equals("outm1") || a.equals("outmapped") || a.equals("outmapped1")){
add(b, outm1List);
args[i]=null;
}else if(a.equals("outm2") || a.equals("outmapped2")){
add(b, outm2List);
args[i]=null;
}else if(a.equals("outu") || a.equals("outu1") || a.equals("outunmapped") || a.equals("outunmapped1")){
add(b, outu1List);
args[i]=null;
}else if(a.equals("outu2") || a.equals("outunmapped2")){
add(b, outu2List);
args[i]=null;
}else if(a.equals("outmlist") || a.equals("outm1list") || a.equals("outmappedlist") || a.equals("outmapped1list")){
addFileContents(b, outm1List);
args[i]=null;
}else if(a.equals("outm2list") || a.equals("outmapped2list")){
addFileContents(b, outm2List);
args[i]=null;
}else if(a.equals("outulist") || a.equals("outu1list") || a.equals("outunmappedlist") || a.equals("outunmapped1list")){
addFileContents(b, outu1List);
args[i]=null;
}else if(a.equals("outu2list") || a.equals("outunmapped2list")){
addFileContents(b, outu2List);
args[i]=null;
}else if(a.equals("outb") || a.equals("outb1") || a.equals("outblack") || a.equals("outblack1") || a.equals("outblacklist") || a.equals("outblacklist1")){
add(b, outb1List);
args[i]=null;
}else if(a.equals("outb2") || a.equals("outblack2") || a.equals("outblacklist2")){
add(b, outb2List);
args[i]=null;
}else if(a.equals("qualityhistogram") || a.equals("qualityhist") || a.equals("qhist")){
add(b, qhistList);
args[i]=null;
}else if(a.equals("matchhistogram") || a.equals("matchhist") || a.equals("mhist")){
add(b, mhistList);
args[i]=null;
}else if(a.equals("inserthistogram") || a.equals("inserthist") || a.equals("ihist")){
add(b, ihistList);
args[i]=null;
}else if(a.equals("bamscript") || a.equals("bs")){
add(b, bsList);
args[i]=null;
}else if(a.equals("append") || a.equals("app")){
append=Parse.parseBoolean(b);
}
}
ArrayList<String> list=new ArrayList<String>();
for(String s : args){
if(s!=null){
list.add(s);
}
}
// return list.toArray(new String[list.size()]);
return list;
}
private static void add(String s, ArrayList<String> list){
if(s!=null && !"null".equals(s.toLowerCase())){
String[] sa=s.split(",");
for(String ss : sa){
list.add(ss);
}
}
}
private static void addFileContents(String s, ArrayList<String> list){
if(s!=null && !"null".equals(s.toLowerCase())){
String[] sa=TextFile.toStringLines(s);
for(String ss : sa){
list.add(ss);
}
}
}
private void execute(ArrayList<String> base){
for(int i=0; i<in1List.size(); i++){
ArrayList<String> list=(ArrayList<String>) base.clone();
if(i==0 && ref!=null){list.add("ref="+ref);}
else if(i>0){list.add("indexloaded=t");}
addToList(list, bsList, "bs", i);
addToList(list, qhistList, "qhist", i);
addToList(list, mhistList, "mhist", i);
addToList(list, ihistList, "ihist", i);
addToList(list, in1List, "in", i);
addToList(list, out1List, "out", i);
addToList(list, outu1List, "outu", i);
addToList(list, outm1List, "outm", i);
addToList(list, outb1List, "outb", i);
addToList(list, in2List, "in2", i);
addToList(list, out2List, "out2", i);
addToList(list, outu2List, "outu2", i);
addToList(list, outm2List, "outm2", i);
addToList(list, outb2List, "outb2", i);
String[] args=list.toArray(new String[list.size()]);
if(mapper==null || mapper.equalsIgnoreCase("bbmap")){
BBMap.main(args);
}else if(mapper.equalsIgnoreCase("bbmappacbio") || mapper.equalsIgnoreCase("pacbio")){
BBMapPacBio.main(args);
}else if(mapper.equalsIgnoreCase("bbmappacbioskimmer") || mapper.equalsIgnoreCase("pacbioskimmer") || mapper.equalsIgnoreCase("skimmer") || mapper.equalsIgnoreCase("bbmapskimmer")){
BBMapPacBioSkimmer.main(args);
}else if(mapper.equalsIgnoreCase("bbmap5") || mapper.equalsIgnoreCase("5")){
BBMap5.main(args);
}else if(mapper.equalsIgnoreCase("bbmapacc") || mapper.equalsIgnoreCase("acc")){
BBMapAcc.main(args);
}else if(mapper.equalsIgnoreCase("bbsplit") || mapper.equalsIgnoreCase("bbsplitter")){
BBSplitter.main(args);
}
}
}
private void addToList(ArrayList<String> list, ArrayList<String> source, String key, int i){
if(source.size()>i){
list.add(key+"="+source.get(i));
}else if(append && source.size()==1){
list.add(key+"="+source.get(0));
}
}
private String ref;
private String mapper="bbmap";
private ArrayList<String> bsList=new ArrayList<String>();
private ArrayList<String> qhistList=new ArrayList<String>();
private ArrayList<String> mhistList=new ArrayList<String>();
private ArrayList<String> ihistList=new ArrayList<String>();
private ArrayList<String> in1List=new ArrayList<String>();
private ArrayList<String> out1List=new ArrayList<String>();
private ArrayList<String> outu1List=new ArrayList<String>();
private ArrayList<String> outm1List=new ArrayList<String>();
private ArrayList<String> outb1List=new ArrayList<String>();
private ArrayList<String> in2List=new ArrayList<String>();
private ArrayList<String> out2List=new ArrayList<String>();
private ArrayList<String> outu2List=new ArrayList<String>();
private ArrayList<String> outm2List=new ArrayList<String>();
private ArrayList<String> outb2List=new ArrayList<String>();
private boolean append=false;
static PrintStream outstream=System.err;
}
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