VCFparser.java

//--- Java imports ---
import java.util.*;
import java.util.zip.*;
import java.io.*;
import java.lang.reflect.*;

class VCFparser {
	private FileInputStream _fin = null;
	private BufferedReader _br = null;
	private String _line = "";
	private int _id_ind = -1;
	private String _id = "";
	private boolean _pass = false;

	public VCFparser(String fileName, String id, boolean pass) {
		try {
			_fin = new FileInputStream(fileName);
			InputStream is = _fin;
			String tmp = new String(fileName);
			tmp.toLowerCase();
			if (tmp.endsWith(".gz") || tmp.endsWith(".gzip"))
				is = new GZIPInputStream(_fin);
			_br = new BufferedReader(new InputStreamReader(is));
			readLine();
		} catch (Exception ex) {
			System.err.println("Can't open file " + fileName);
			System.err.println(ex.toString());
		}
		if (id != null)
			_id = id;
		_pass = pass;
	}

	public boolean hasMoreInput() {
		return (_line != null);
	}

	public Variant parseLine() {
		String line = _line;
		readLine();

		if (line == null || line.length() == 0)
			return null;

		StringTokenizer toks = new StringTokenizer(line);
		if (line.startsWith("#")) {
			if (line.startsWith("#CHROM")) {
				int index = 0;
				while (toks.hasMoreTokens()) {
					index++;
					String tok = toks.nextToken();
					if (tok.equals(_id))
						_id_ind = index;
				}
			}
			return null;
		}

		int index = 0, genotype_ind = -1;
		String chr = "";
		int pos = -1;
		String REF = "", FILTER = "", ALT = "", phase = "0/0", INFO = "";
		while (toks.hasMoreTokens()) {
			index++;
			if (index == 1) // Parsing chromosome
				chr = toks.nextToken();
			else if (index == 2) // Parsing position
				pos = Integer.parseInt(toks.nextToken());
			else if (index == 4) // Parsing reference allele
				REF = toks.nextToken();
			else if (index == 5) // Parsing alternative allele
				ALT = toks.nextToken();
			else if (index == 7) // FILTER field
				FILTER = toks.nextToken();
			// else if (index == 8) // INFO field
			// INFO = toks.nextToken();
			else if (index == 9) { // Output format
				genotype_ind = getGenotypeIndex(toks.nextToken());
				if (genotype_ind < 0)
					break;
			} else if (index == _id_ind) { // Phasing
				StringTokenizer words = new StringTokenizer(toks.nextToken(), ":");
				phase = words.nextToken();
				break;
			} else
				toks.nextToken();
		}

		if (ALT.equals("<DEL>")) {
			System.out.println("Skipping record with ALT = <DEL>");
			return null; // Imprecise SV
		}
		if (_pass && FILTER.indexOf("PASS") < 0) {
			System.out.println("Skipping record with FILTER = " + FILTER);
			return null; // Filtered out
		}

		// Upper casing
		REF = REF.toUpperCase();
		ALT = ALT.toUpperCase();

		// Splitting
		String[] alts = ALT.split(",");
		int n = alts.length;

		// Check
		for (int i = 0; i < n; i++)
			if (REF.length() == 1 && alts[i].length() == 1)
				; // SNP
			else if (REF.length() == 0 || alts[i].length() == 0) {
				System.err.println("Skipping invalid record:");
				System.err.println(" " + line);
				return null;
			}

		// Adjustment of first base
		if (REF.length() > 0) {
			boolean same = true;
			for (int i = 0; i < n; i++)
				if (alts[i].length() == 0 ||
						REF.charAt(0) != alts[i].charAt(0)) {
					same = false;
					break;
				}
			if (same) {
				pos++;
				REF = REF.substring(1);
				for (int i = 0; i < n; i++)
					alts[i] = alts[i].substring(1);
			}
		}

		// Adjustment of last
		if (REF.length() > 0) {
			boolean same = true;
			int indREF = REF.length() - 1;
			for (int i = 0; i < n; i++) {
				int len = alts[i].length();
				if (len == 0 ||
						REF.charAt(indREF) != alts[i].charAt(len - 1)) {
					same = false;
					break;
				}
			}
			if (same) {
				REF = REF.substring(0, indREF);
				for (int i = 0; i < n; i++)
					alts[i] = alts[i].substring(0, alts[i].length() - 1);
			}

			// System.out.print(REF);
			// for (int i = 0;i < n;i++)
			// System.out.print(" " + alts[i]);
			// System.out.println(pos);
		}
		return new Variant(chr, pos, REF.length(), alts, phase);
	}

	private void readLine() {
		_line = null;
		try {
			_line = _br.readLine();
		} catch (Exception ex) {
		}

		if (_line == null) {
			try {
				_br.close();
				_fin.close();
			} catch (Exception ex) {
			}
			_br = null;
			_fin = null;
		}
	}

	private int getGenotypeIndex(String record) {
		StringTokenizer words = new StringTokenizer(record, ":");
		int ret = 0;
		while (words.hasMoreTokens())
			if (words.nextToken().equals("GT"))
				return ret;
			else
				ret++;
		return -1;
	}
}