Walker to pull out the reference for given intervals and emit them in fasta format

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@843 348d0f76-0448-11de-a6fe-93d51630548a

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

@@ -0,0 +1,58 @@
+package org.broadinstitute.sting.playground.gatk.walkers;
+
+import org.broadinstitute.sting.gatk.LocusContext;
+import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
+import org.broadinstitute.sting.gatk.walkers.RefWalker;
+import org.broadinstitute.sting.gatk.walkers.WalkerName;
+import org.broadinstitute.sting.utils.GenomeLoc;
+import org.broadinstitute.sting.utils.Pair;
+
+// create a fasta sequence file from a reference and intervals
+
+@WalkerName("FastaReferenceMaker")
+public class FastaReferenceWalker extends RefWalker<Pair<GenomeLoc, Character>, Pair<GenomeLoc, String>> {
+
+	public Pair<GenomeLoc, Character> map(RefMetaDataTracker rodData, char ref, LocusContext context) {
+        return new Pair<GenomeLoc, Character>(context.getLocation(), ref);
+	}
+
+    public Pair<GenomeLoc, String> reduceInit() {
+        return new Pair<GenomeLoc, String>(null, "");
+    }
+
+	public Pair<GenomeLoc, String> reduce(Pair<GenomeLoc, Character> value, Pair<GenomeLoc, String> sum) {
+        // if there is no interval to the left, then this is the first one
+        if ( sum.first == null ) {
+            sum.first = value.first;
+            sum.second = value.second.toString();
+        }
+        // if the intervals don't overlap, print out the leftmost one and start a new one
+        else if ( value.first.getStart() != sum.first.getStop() + 1 ) {
+            printFasta(sum.first, sum.second);
+            sum.first = value.first;
+            sum.second = value.second.toString();
+        }
+        // otherwise, merge them
+        else {
+            sum.first.setStop(value.first.getStop());
+            sum.second = new String(sum.second + value.second);
+        }
+		return sum;
+	}
+
+    public void onTraversalDone(Pair<GenomeLoc, String> sum) {
+        if (sum.second != null)
+            printFasta(sum.first, sum.second);
+    }
+
+    private void printFasta(GenomeLoc loc, String s) {
+        out.println(">" + loc);
+        int lines = s.length() / 60;
+        int currentStart = 0;
+        for (int i=0; i < lines; i++) {
+            out.println(s.substring(currentStart, currentStart+60));
+            currentStart += 60;
+        }
+        out.println(s.substring(currentStart));
+    }
+}