Simple tool for picking sequenom probes for SNPs. Can be extended to indels if necessary.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1780 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/PickSequenomProbes.java

@@ -0,0 +1,108 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
+import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
+import org.broadinstitute.sting.gatk.refdata.*;
+import org.broadinstitute.sting.gatk.walkers.*;
+import org.broadinstitute.sting.utils.*;
+import org.broadinstitute.sting.utils.cmdLine.Argument;
+import org.broadinstitute.sting.utils.genotype.Variation;
+
+import java.io.*;
+import java.util.*;
+
+
+@WalkerName("PickSequenomProbes")
+@Requires(value={DataSource.REFERENCE})
+@Reference(window=@Window(start=-200,stop=200))
+public class PickSequenomProbes extends RefWalker<String, String>
+{
+    @Argument(required=false, shortName="snp_mask", doc="positions to be masked with N's") public String SNP_MASK = null;
+
+	ArrayList<GenomeLoc> mask = null;
+	Object[] mask_array = null;
+    public void initialize() 
+	{
+		System.out.printf("Loading SNP mask...  ");
+		if (SNP_MASK != null)
+		{
+	         mask = new ArrayList<GenomeLoc>();
+			 mask.addAll(GenomeLocParser.intervalFileToList(SNP_MASK));
+
+			 Object[] temp_array = mask.toArray();
+			 mask_array = new GenomeLoc[temp_array.length];
+			 for (int i = 0; i < temp_array.length; i++) { mask_array[i] = (GenomeLoc)temp_array[i]; }
+			 Arrays.sort(mask_array);
+		}
+		System.out.printf("Done.\n");
+    }
+
+	private boolean in_mask(GenomeLoc loc)
+	{
+		return (Arrays.binarySearch(mask_array, loc) >= 0);
+	}
+
+    public String map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) 
+	{
+        String refBase = String.valueOf(ref.getBase());
+
+		System.out.printf("Probing " + ref.getLocus() + " " + ref.getWindow() + "\n");
+
+        Iterator<ReferenceOrderedDatum> rods = rodData.getAllRods().iterator();
+
+		Variation snp = null;
+        while (rods.hasNext()) 
+		{
+            ReferenceOrderedDatum rod = rods.next();
+            if (!(rod instanceof Variation))
+                continue;
+
+            Variation variant = (Variation) rod;
+            if (variant.isSNP())
+			{
+				snp = variant;
+            }
+        }
+
+		String contig = context.getLocation().getContig();
+		long   offset = context.getLocation().getStart();
+
+		char[] context_bases = ref.getBases();
+		long true_offset = offset - 400; 
+		for (long i = 0; i < 401; i++)
+		{
+			GenomeLoc loc = GenomeLocParser.parseGenomeLoc(context.getLocation().getContig() + ":" + true_offset + "-" + true_offset);
+			if (in_mask(loc)) { context_bases[(int)i] = 'N'; }
+			true_offset += 1;
+		}
+		char[] leading_bases  = Arrays.copyOfRange(context_bases, 0, 200);
+		char[] trailing_bases = Arrays.copyOfRange(context_bases, 201, 401);
+
+		if (snp != null) 
+		{
+			String snp_string = new String(leading_bases) + new String("[" + refBase + "/" + snp.getAlternativeBaseForSNP() + "]") + new String(trailing_bases);
+			String fasta_string = new String(">" + context.getLocation().toString() + "_" + ref.getWindow().toString());
+			return fasta_string + "\n" + snp_string + "\n";
+		}
+		else
+		{
+			return "";
+		}
+    }
+
+	public String reduceInit()
+	{
+		return "";
+	}
+
+	public String reduce(String data, String sum)
+	{
+		out.print(data);
+		return "";
+	}
+
+    public void onTraversalDone(String sum) 
+	{
+    }
+
+}