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package driver;
import java.io.OutputStream;
import java.io.PrintWriter;
import fileIO.ReadWrite;
import fileIO.TextFile;
public class ConvertSamToAln {
public static void main(String[] args){
for(String s : args){
convert(s);
System.out.println("Converted "+s);
}
}
public static final void convert(String fname){
TextFile tf=new TextFile(fname, false);
String outname=fname;
if(outname.toLowerCase().endsWith(".zip")){outname=outname.substring(0, outname.length()-4);}
if(outname.toLowerCase().endsWith(".gz")){outname=outname.substring(0, outname.length()-3);}
if(outname.toLowerCase().endsWith(".bz2")){outname=outname.substring(0, outname.length()-4);}
if(outname.toLowerCase().endsWith(".sam")){outname=outname.substring(0, outname.length()-4);}
outname=outname+".aln.gz";
String s=null;
OutputStream os=ReadWrite.getOutputStream(outname, false, true, true);
PrintWriter out=new PrintWriter(os);
for(s=tf.nextLine(); s!=null; s=tf.nextLine()){
if(!s.startsWith("@")){
String[] line=s.split("\t");
assert(line.length>1) : s;
boolean success=true;
boolean nomap=false;
boolean reverse=false;
int flag=-1;
String chrom=null;
int loc=-1;
try {
flag=Integer.parseInt(line[1]);
chrom=line[2];
loc=Integer.parseInt(line[3]);
nomap=((flag&0x4)!=0);
reverse=((flag&0x10)!=0);
} catch (NumberFormatException e) {
success=false;
}
if(success && !nomap){
String aln=chrom+"\t"+loc+"\t"+(reverse ? "R" : "F")+"\n";
out.print(aln);
}
}
}
tf.close();
out.flush();
out.close();
}
}
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