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/*
* Copyright (C) 2014-2021 Brian L. Browning
*
* This file is part of Beagle
*
* Beagle is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* Beagle is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package bref;
import blbutil.Const;
import blbutil.FileIt;
import blbutil.InputIt;
import blbutil.SampleFileIt;
import blbutil.Utilities;
import java.io.File;
import vcf.RefGTRec;
import vcf.RefIt;
import vcf.Samples;
/**
* <p>Class {@code Bref3} converts files in VCF format into
* bref version 3 format.
* </p>
* <p>Instances of class {@code Bref3} are not thread-safe.</p>
*
* @author Brian L. Browning {@code <browning@uw.edu>}
*/
public class Bref3 {
private static final String program = "bref3.22Jul22.46e.jar";
/**
* The {@code main()} method is the entry point to the bref program.
* See the usage() method for usage instructions.
*
* @param args the command line arguments
*/
public static void main(String[] args) {
if (args.length>2) {
System.out.println(usage());
System.exit(0);
}
if (args.length==1 && args[0].equalsIgnoreCase("help")) {
System.out.println(usage());
System.exit(0);
}
boolean useStdIn = useStdIn(args);
int maxNSeq = -1;
if (args.length==2 || (useStdIn && args.length==1)) {
maxNSeq = maxNSeq(args[args.length-1]);
}
String inputFile = useStdIn ? null : args[0];
writeBref(inputFile, maxNSeq);
}
private static boolean useStdIn(String[] sa) {
if (sa.length==0) {
return true;
}
else if (sa.length==1) {
return (sa[0].endsWith(".vcf") || sa[0].endsWith(".vcf.gz"))==false;
}
else {
return false;
}
}
private static int maxNSeq(String arg) {
int maxNSeq = -1;
try {
maxNSeq = Integer.parseInt(arg);
if (maxNSeq < 1 || maxNSeq > Character.MAX_VALUE) {
exit("Error: invalid <nSeq> " + arg);
}
}
catch (NumberFormatException e) {
exit("Error: <nSeq> is not a parsable integer: " + arg);
}
return maxNSeq;
}
private static void exit(String msg) {
System.out.println(usage());
Utilities.exit(msg);
}
private static void writeBref(String fileName, int maxNSeq) {
try (SampleFileIt<RefGTRec> it = refIt(fileName);
BrefWriter brefOut = brefOut(it.samples(), maxNSeq)) {
while (it.hasNext()) {
brefOut.write(it.next());
}
}
}
private static SampleFileIt<RefGTRec> refIt(String fileName) {
FileIt<String> it = null;
if (fileName==null) {
it = InputIt.fromStdIn();
}
else if (fileName.endsWith(".gz")) {
it = InputIt.fromGzipFile(new File(fileName));
}
else {
it = InputIt.fromTextFile(new File(fileName));
}
return RefIt.create(it);
}
private static BrefWriter brefOut(Samples samples, int maxNSeq) {
File outFile = null; // write to standard output
if (maxNSeq<0) {
return new AsIsBref3Writer(program, samples, outFile);
}
else {
return new CompressBref3Writer(program, samples, maxNSeq, outFile);
}
}
private static String usage() {
StringBuilder sb = new StringBuilder(500);
sb.append("usage:");
sb.append(Const.nl);
sb.append(" java -jar ");
sb.append(program);
sb.append(" help");
sb.append(Const.nl);
sb.append(Const.nl);
sb.append(" java -jar ");
sb.append(program);
sb.append(" [vcf] <nseq> > [bref3]");
sb.append(Const.nl);
sb.append(Const.nl);
sb.append(" cat [vcf] | java -jar ");
sb.append(program);
sb.append(" <nseq> > [bref3]");
sb.append(Const.nl);
sb.append(Const.nl);
sb.append("where");
sb.append(Const.nl);
sb.append(" [bref3] = the output bref3 file");
sb.append(Const.nl);
sb.append(" [vcf] = A VCF file with phased, non-missing genotype data. If the");
sb.append(Const.nl);
sb.append(" file is gzip-compressed, its filename must end in \".gz\"");
sb.append(Const.nl);
sb.append(" and \"cat\" must be replaced with \"zcat\"");
sb.append(Const.nl);
sb.append(" <nseq> = optional argument for maximum number of unique sequences");
sb.append(Const.nl);
sb.append(" in a bref3 block. If there are N reference samples,");
sb.append(Const.nl);
sb.append(" the default value is: <max-seq>=2^(2*log10(N) + 1)");
sb.append(Const.nl);
return sb.toString();
}
}
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