- moved the reference maker to its own directory

- added first version of a more complicated reference maker which takes in RODs and creates an alternative reference based on the variants (indels and/or SNPs)


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1409 348d0f76-0448-11de-a6fe-93d51630548a

java/src/org/broadinstitute/sting/playground/gatk/walkers/fasta/FastaAlternateReferenceWalker.java

@@ -0,0 +1,89 @@
+package org.broadinstitute.sting.playground.gatk.walkers.fasta;
+
+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 java.util.Iterator;
+
+// create a fasta sequence file from a reference, intervals, and rod(s) of variants
+
+@WalkerName("FastaAlternateReferenceMaker")
+@Requires(value={DataSource.REFERENCE})
+public class FastaAlternateReferenceWalker extends RefWalker<Pair<GenomeLoc, String>, Pair<GenomeLoc, String>> {
+
+	private StringBuffer sb = new StringBuffer();
+    int deletionBasesRemaining = 0;
+
+    public Pair<GenomeLoc, String> map(RefMetaDataTracker rodData, ReferenceContext ref, AlignmentContext context) {
+        if ( deletionBasesRemaining > 0 ) {
+            deletionBasesRemaining--;
+            return new Pair<GenomeLoc, String>(context.getLocation(), "");
+        }
+
+        Iterator<ReferenceOrderedDatum> rods = rodData.getAllRods().iterator();
+        while ( rods.hasNext() ) {
+            ReferenceOrderedDatum rod = rods.next();
+            if ( !(rod instanceof AllelicVariant) )
+                continue;
+
+            // if we have multiple variants at a locus, just take the first damn one we see for now
+            AllelicVariant variant = (AllelicVariant)rod;
+            if ( variant.isDeletion() ) {
+                deletionBasesRemaining = variant.length();
+                // delete the next n bases, not this one
+                return new Pair<GenomeLoc, String>(context.getLocation(), String.valueOf(ref.getBase()));
+            } else if ( variant.isInsertion() ) {
+                return new Pair<GenomeLoc, String>(context.getLocation(), String.valueOf(ref.getBase()).concat(variant.getAltBasesFWD()));
+            } else if ( variant.isSNP() ) {
+                return new Pair<GenomeLoc, String>(context.getLocation(), variant.getAltBasesFWD());
+            }
+        }
+
+        // if we got here then we're just ref
+        return new Pair<GenomeLoc, String>(context.getLocation(), String.valueOf(ref.getBase()));
+	}
+
+    public Pair<GenomeLoc, String> reduceInit() {
+        return new Pair<GenomeLoc, String>(null, "");
+    }
+
+	public Pair<GenomeLoc, String> reduce(Pair<GenomeLoc, String> 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;
+        }
+        // if the intervals don't overlap, print out the leftmost one and start a new one
+        // (end of contig or new interval)
+        else if ( value.first.getStart() != sum.first.getStop() + 1 ) {
+            printFasta(sum.first, sum.second);
+            sum.first = value.first;
+            sum.second = value.second;
+        }
+        // otherwise, merge them
+        else {
+            sum.first = GenomeLocParser.setStop(sum.first,value.first.getStop());
+            sum.second = sum.second.concat(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));
+    }
+}

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

@@ -1,4 +1,4 @@
-package org.broadinstitute.sting.playground.gatk.walkers;
+package org.broadinstitute.sting.playground.gatk.walkers.fasta;
 
 import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
 import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
@@ -29,6 +29,7 @@ public class FastaReferenceWalker extends RefWalker<Pair<GenomeLoc, Character>,
             sum.second = value.second.toString();
         }
         // if the intervals don't overlap, print out the leftmost one and start a new one
+        // (end of contig or new interval)
         else if ( value.first.getStart() != sum.first.getStop() + 1 ) {
             printFasta(sum.first, sum.second);
             sum.first = value.first;