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package gff;
import java.io.PrintStream;
import fileIO.ByteFile;
import fileIO.ByteStreamWriter;
import fileIO.FileFormat;
import shared.Parser;
import shared.PreParser;
import shared.Timer;
import shared.Tools;
import structures.ByteBuilder;
import tracker.ReadStats;
import var2.VCFLine;
/**
* Stripped out of GffLine into independent class.
* @author Brian Bushnell
* @date Sep 12, 2018
*
*/
public class VcfToGff {
/** Translates VCF to GFF */
public static void main(String[] args){
Timer t=new Timer();
PrintStream outstream=System.err;
{//Preparse block for help, config files, and outstream
PreParser pp=new PreParser(args, new Object() { }.getClass().getEnclosingClass(), false);
args=pp.args;
outstream=pp.outstream;
t.outstream=outstream;
}
Parser parser=new Parser();
String in=null;
String out=null;
boolean overwrite=true, append=false;
//Parse each argument
for(int i=0; i<args.length; i++){
String arg=args[i];
//Break arguments into their constituent parts, in the form of "a=b"
String[] split=arg.split("=");
String a=split[0].toLowerCase();
String b=split.length>1 ? split[1] : null;
if(a.equals("in") || a.equals("vcf")){
in=b;
}else if(a.equals("out") || a.equals("gff")){
out=b;
}else if(parser.parse(arg, a, b)){
//do nothing
}else if(in==null && b==null && i==0 && Tools.canRead(arg)){
in=arg;
}else if(in==null && b==null && i==1){
out=arg;
}else{
outstream.println("Unknown parameter "+args[i]);
assert(false) : "Unknown parameter "+args[i];
}
}
{//Process parser fields
overwrite=ReadStats.overwrite=parser.overwrite;
append=ReadStats.append=parser.append;
}
//Ensure output files can be written
if(!Tools.testOutputFiles(overwrite, append, false, out)){
outstream.println((out==null)+", "+out);
throw new RuntimeException("\n\noverwrite="+overwrite+"; Can't write to output files "+out+"\n");
}
//Ensure input files can be read
if(!Tools.testInputFiles(false, true, in)){
throw new RuntimeException("\nCan't read some input files.\n");
}
//Ensure that no file was specified multiple times
if(!Tools.testForDuplicateFiles(true, in, out)){
throw new RuntimeException("\nSome file names were specified multiple times.\n");
}
translate(in, out, overwrite, append);
t.stop("Time: \t");
}
/** Translates VCF to GFF */
private static void translate(String in, String out, boolean overwrite, boolean append){
//Create output FileFormat objects
FileFormat ffout=FileFormat.testOutput(out, FileFormat.GFF, "gff", true, overwrite, append, false);
//Create input FileFormat objects
FileFormat ffin=FileFormat.testInput(in, FileFormat.VCF, "vcf", true, true);
ByteFile bf=ByteFile.makeByteFile(ffin);
ByteStreamWriter bsw=null;
if(ffout!=null){
bsw=new ByteStreamWriter(ffout);
bsw.start();
}
ByteBuilder bb=new ByteBuilder(17000);
bb.append("##gff-version 3\n");
String header="#seqid source type start end score strand phase attributes";
for(byte[] line=bf.nextLine(); line!=null; line=bf.nextLine()){
if(line.length>1){
if(line[0]=='#'){
if(Tools.startsWith(line, "##fileformat") || Tools.startsWith(line, "##FORMAT") ||
Tools.startsWith(line, "##INFO") || Tools.startsWith(line, "#CHROM POS")){
//skip
}else{
int i=1;
while(i<line.length && line[i]=='#'){i++;}
i--;
bb.append(line, i, line.length-i);
bb.nl();
}
}else{
if(header!=null){
bb.append(header).append('\n');
header=null;
}
VCFLine vline=new VCFLine(line);
GffLine gline=new GffLine(vline);
gline.appendTo(bb);
bb.nl();
}
}
if(bb.length()>=16384){
if(bsw!=null){
bsw.print(bb);
}
bb.clear();
}
}
if(bb.length()>0){
if(bsw!=null){
bsw.print(bb);
}
bb.clear();
}
bf.close();
if(bsw!=null){bsw.poisonAndWait();}
}
}
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