Naive tool to convert from vcf to geli text

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1606 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/tools/VcfToGeliText.java

@@ -0,0 +1,93 @@
+package org.broadinstitute.sting.playground.tools;
+
+import net.sf.picard.cmdline.CommandLineProgram;
+import net.sf.picard.cmdline.Usage;
+import net.sf.picard.cmdline.Option;
+
+import java.io.*;
+import java.util.*;
+
+public class VcfToGeliText extends CommandLineProgram {
+    @Usage(programVersion="1.0") public String USAGE = "Converts VCF files to simple Geli text files.";
+    @Option(shortName="I", doc="Input file (vcf) to convert.", optional=false) public File IN = null;
+    @Option(shortName="O",doc="Output file (gelitext). If not specified, output is printed to stdout.", optional=true) public File OUT = null;
+    @Option(shortName="sample",doc="Sample number to extract from the VCF. If not specified, it takes the firt one.", optional=true) public Integer sample = 1;
+
+    public static void main(final String[] argv) {
+        System.exit(new VcfToGeliText().instanceMain(argv));
+    }
+
+    protected int doWork() {
+
+        if ( IN == null )
+            throw new RuntimeException("No input VCF file provided!");
+
+        FileReader in;
+        BufferedReader vcf;
+        try {
+            in = new FileReader(IN);
+            vcf = new BufferedReader(in);
+        } catch ( FileNotFoundException ie ) {
+            System.out.println("Failed to open input file "+IN+": "+ie.getCause());
+            return 1;
+        }
+
+        PrintStream out;
+        if ( OUT == null ) out = System.out;
+        else {
+            try {
+                out =  new PrintStream(OUT);
+            } catch ( FileNotFoundException ie ) {
+                System.out.println("Failed to open output file "+OUT+": "+ie.getCause());
+                return 1;
+            }
+        }
+
+        String currentline;
+        try {
+            while ( (currentline = vcf.readLine()) != null ) {
+                if ( currentline.length() == 0 || currentline.charAt(0) == '#' )
+                    continue;
+
+                StringTokenizer st = new StringTokenizer(currentline);
+                String chr = st.nextToken();
+                String pos = st.nextToken();
+                st.nextToken();
+                String ref = st.nextToken();
+                String altStr = st.nextToken();
+                for (int i = 0; i < 4; i++)
+                    st.nextToken();
+                for (int i = 1; i < sample; i++)
+                    st.nextToken();
+                String sampleStr = st.nextToken();
+
+                HashMap<String,String> alleles = new HashMap<String,String>();
+                alleles.put("0", ref);
+                StringTokenizer stAlt = new StringTokenizer(altStr, ",");
+                int index = 1;
+                while ( stAlt.hasMoreTokens() )
+                    alleles.put(String.valueOf(index++), stAlt.nextToken());
+
+                StringTokenizer stSample = new StringTokenizer(sampleStr, "/:");
+                String genotype1 = stSample.nextToken();
+                String genotype2 = stSample.nextToken();
+                if ( genotype1.equals("0") && genotype2.equals("0") )
+                    continue;
+
+                out.println(chr + "\t" + pos + "\t" + ref + "\t0\t0\t"
+                        + alleles.get(genotype1) + alleles.get(genotype2)
+                        + "\t30\t30\t0\t0\t0\t0\t0\t0\t0\t0\t0\t0");
+            }
+            vcf.close();
+            in.close();
+            out.close();
+        } catch (IOException e) {
+            System.out.println("Jaa I/O exception"+e.getCause());
+            return 1;
+        }
+
+        return 0;
+    }
+
+
+}