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package jgi;
import java.io.File;
import java.util.ArrayList;
import fileIO.ByteStreamWriter;
import fileIO.FileFormat;
import shared.Parser;
import shared.PreParser;
import shared.Shared;
import shared.Timer;
import shared.Tools;
import structures.ByteBuilder;
/**
* Generates some stats from multiple files.
* Uses the new Assembly class.
* @author Brian Bushnell
* @date January 21, 2025
*
*/
public class AssemblyStats3 {
public static void main(String[] args){
//Start a timer immediately upon code entrance.
Timer t=new Timer();
//Create an instance of this class
AssemblyStats3 x=new AssemblyStats3(args);
//Run the object
x.process(t);
//Close the print stream if it was redirected
Shared.closeStream(x.outstream);
}
public AssemblyStats3(String[] args){
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, getClass(), false);
args=pp.args;
outstream=pp.outstream;
}
Parser parser=new Parser();
parser.out1=out1;
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(b!=null && b.equalsIgnoreCase("null")){b=null;}
if(a.equals("parse_flag_goes_here")){
//Set a variable here
}else if(a.equals("in")){
in.clear();
String[] b2=(b==null) ? null : (new File(b).exists() ? new String[] {b} : b.split(","));
for(String b3 : b2){in.add(b3);}
}else if(b==null && new File(arg).exists()){
in.add(arg);
}else if(parser.parse(arg, a, b)){
//do nothing
}else{
assert(false) : "Unknown parameter "+args[i];
outstream.println("Unknown parameter "+args[i]);
}
}
{//Process parser fields
Parser.processQuality();
maxReads=parser.maxReads;
out1=parser.out1;
}
ffout1=FileFormat.testOutput(out1, FileFormat.TXT, null, true, true, false, false);
}
void process(Timer t){
final ByteStreamWriter bsw=ByteStreamWriter.makeBSW(ffout1);
if(bsw!=null) {bsw.println(makeHeader());}
for(String s : in) {
processInner(s, bsw);
}
if(bsw!=null) {bsw.poisonAndWait();}
if(verbose){outstream.println("Finished.");}
t.stop();
Tools.timeLinesBytesProcessed(t, linesProcessed, bytesProcessed, 12);
}
public static String makeHeader() {
ByteBuilder bb=new ByteBuilder();
bb.append("fname");
bb.tab().append("size");
bb.tab().append("contigs");
bb.tab().append("gc");
bb.tab().append("maxContig");
bb.tab().append("5kplus");
bb.tab().append("10kplus");
bb.tab().append("25kplus");
bb.tab().append("50kplus");
return bb.toString();
}
void processInner(String fname, ByteStreamWriter bsw) {
Assembly a=new Assembly(fname);
if(bsw==null) {return;}
int max=a.contigs.size>0 ? a.contigs.get(0) : 0;
bsw.print(fname).tab().print(a.length).tab().print(a.contigs.size);
bsw.tab().print(a.gc(), 3).tab().print(max);
bsw.tab().print(a.lengthAtLeast(5000));
bsw.tab().print(a.lengthAtLeast(10000));
bsw.tab().print(a.lengthAtLeast(25000));
bsw.tab().print(a.lengthAtLeast(50000));
bsw.nl();
}
/*--------------------------------------------------------------*/
/*--------------------------------------------------------------*/
private ArrayList<String> in=new ArrayList<String>();
private String out1="stdout.txt";
private final FileFormat ffout1;
/*--------------------------------------------------------------*/
private long maxReads=-1;
private long linesProcessed=0, bytesProcessed=0;
/*--------------------------------------------------------------*/
private java.io.PrintStream outstream=System.err;
public static boolean verbose=false;
}
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